Starting phenix.real_space_refine
on Sat Aug 23 09:15:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h95_34555/08_2025/8h95_34555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h95_34555/08_2025/8h95_34555.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h95_34555/08_2025/8h95_34555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h95_34555/08_2025/8h95_34555.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h95_34555/08_2025/8h95_34555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h95_34555/08_2025/8h95_34555.cif"
  }
  resolution = 3.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      91      5.16       5
     C    7057      2.51       5
     N    1898      2.21       5
     O    2052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11098
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 949, 7481
          Classifications: {'peptide': 949}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 26, 'TRANS': 922}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 2898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2898
          Classifications: {'peptide': 367}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 719
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 4, 'TRANS': 84}
  Time building chain proxies: 2.45, per 1000 atoms: 0.22
  Number of scatterers: 11098
  At special positions: 0
  Unit cell: (92.4, 105.6, 132, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      91     16.00
     O    2052      8.00
     N    1898      7.00
     C    7057      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 532.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2672

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 14 sheets defined
      40.1% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 97 through 109
    Processing helix  chain 'A' and resid 119 through 129
      removed outlier: 3.639A  pdb=" N   LYS A 123 " --> pdb=" O   SER A 119 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 125 " --> pdb=" O   GLU A 121 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   PHE A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 165
      removed outlier: 3.678A  pdb=" N   LEU A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 198
    Processing helix  chain 'A' and resid 202 through 211
      removed outlier: 4.595A  pdb=" N   THR A 206 " --> pdb=" O   TRP A 202 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET A 209 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   SER A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 214
      No H-bonds generated for 'chain 'A' and resid 212 through 214'
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 3.854A  pdb=" N   ASP A 226 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   SER A 227 " --> pdb=" O   ASP A 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 223 through 227'
    Processing helix  chain 'A' and resid 246 through 255
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.584A  pdb=" N   LEU A 273 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 302
      removed outlier: 3.637A  pdb=" N   ARG A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
      removed outlier: 3.751A  pdb=" N   ASN A 320 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.833A  pdb=" N   GLN A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 346
    Processing helix  chain 'A' and resid 356 through 373
      removed outlier: 3.534A  pdb=" N   LEU A 360 " --> pdb=" O   THR A 356 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS A 372 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 401
    Processing helix  chain 'A' and resid 406 through 413
      removed outlier: 3.575A  pdb=" N   TYR A 413 " --> pdb=" O   ASP A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 425
      removed outlier: 3.529A  pdb=" N   ILE A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 3.896A  pdb=" N   GLN A 448 " --> pdb=" O   HIS A 444 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   TYR A 456 " --> pdb=" O   ALA A 452 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   VAL A 457 " --> pdb=" O   ALA A 453 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 458 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.010A  pdb=" N   GLN A 466 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 498
    Processing helix  chain 'A' and resid 500 through 512
    Processing helix  chain 'A' and resid 518 through 532
      removed outlier: 4.103A  pdb=" N   LYS A 522 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE A 530 " --> pdb=" O   TRP A 526 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ALA A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 552
      removed outlier: 3.580A  pdb=" N   SER A 552 " --> pdb=" O   CYS A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 562
    Processing helix  chain 'A' and resid 574 through 586
      removed outlier: 4.217A  pdb=" N   LYS A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 638
      removed outlier: 3.558A  pdb=" N   GLU A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 664
      removed outlier: 3.717A  pdb=" N   MET A 657 " --> pdb=" O   SER A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing helix  chain 'A' and resid 684 through 693
      removed outlier: 3.974A  pdb=" N   PHE A 693 " --> pdb=" O   TRP A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 721
    Processing helix  chain 'A' and resid 738 through 751
    Processing helix  chain 'A' and resid 766 through 779
      removed outlier: 3.825A  pdb=" N   SER A 779 " --> pdb=" O   ASN A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 807
    Processing helix  chain 'A' and resid 823 through 836
      removed outlier: 3.895A  pdb=" N   ASN A 836 " --> pdb=" O   GLN A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 865
      removed outlier: 4.467A  pdb=" N   ASN A 865 " --> pdb=" O   MET A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 892
      removed outlier: 3.887A  pdb=" N   MET A 884 " --> pdb=" O   GLY A 880 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 886 " --> pdb=" O   GLY A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 923
    Processing helix  chain 'A' and resid 936 through 951
      removed outlier: 3.872A  pdb=" N   GLY A 940 " --> pdb=" O   LEU A 936 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A 941 " --> pdb=" O   GLY A 937 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A 947 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLN A 950 " --> pdb=" O   GLU A 946 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   SER A 951 " --> pdb=" O   GLY A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 979
      removed outlier: 3.753A  pdb=" N   CYS A 979 " --> pdb=" O   LEU A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1006
    Processing helix  chain 'A' and resid 1023 through 1037
    Processing helix  chain 'A' and resid 1045 through 1049
      removed outlier: 3.697A  pdb=" N   SER A1049 " --> pdb=" O   TRP A1046 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 174
      removed outlier: 3.503A  pdb=" N   PHE B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG B 174 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 258
    Processing helix  chain 'C' and resid 38 through 42
      removed outlier: 3.589A  pdb=" N   VAL C  41 " --> pdb=" O   ILE C  38 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER C  42 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 38 through 42'
    Processing helix  chain 'C' and resid 51 through 59
    Processing helix  chain 'C' and resid 62 through 73
    Processing helix  chain 'C' and resid 94 through 114
    Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178
      removed outlier: 5.981A  pdb=" N   ILE A 175 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   ASP A 220 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   PHE A 177 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   THR A 140 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   ILE A 286 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 142 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   VAL A 288 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   HIS A 144 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   TYR A 285 " --> pdb=" O   ARG C  32 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG C  28 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188
    Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 432
    Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 571
      removed outlier: 3.630A  pdb=" N   ILE A 594 " --> pdb=" O   GLU A 644 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 596 " --> pdb=" O   ASP A 646 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR A 675 " --> pdb=" O   LEU A 645 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU A 674 " --> pdb=" O   ASN A 702 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   LEU A 701 " --> pdb=" O   ARG A 731 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LEU A 758 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 814 through 816
      removed outlier: 7.110A  pdb=" N   LEU A 815 " --> pdb=" O   ILE A 845 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 873 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LEU A 901 " --> pdb=" O   ASP A 930 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU A 929 " --> pdb=" O   GLY A 959 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987
    Processing sheet with id=AA7, first strand: chain 'B' and resid 283 through 288
      removed outlier: 3.645A  pdb=" N   ALA B 283 " --> pdb=" O   LYS B 580 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   VAL B 576 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B 566 " --> pdb=" O   TYR B 577 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 300
      removed outlier: 4.021A  pdb=" N   VAL B 298 " --> pdb=" O   CYS B 311 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 308 " --> pdb=" O   TRP B 319 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B 318 " --> pdb=" O   SER B 333 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 351
      removed outlier: 7.057A  pdb=" N   GLY B 361 " --> pdb=" O   ARG B 347 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   CYS B 349 " --> pdb=" O   PHE B 359 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   PHE B 359 " --> pdb=" O   CYS B 349 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   LEU B 351 " --> pdb=" O   THR B 357 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   THR B 357 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B 370 " --> pdb=" O   LYS B 381 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASP B 372 " --> pdb=" O   TYR B 379 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   TYR B 379 " --> pdb=" O   ASP B 372 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 394 through 397
      removed outlier: 4.241A  pdb=" N   MET B 401 " --> pdb=" O   THR B 397 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL B 411 " --> pdb=" O   ASN B 424 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   ASN B 424 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ILE B 413 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 434 through 437
      removed outlier: 3.747A  pdb=" N   ASN B 434 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY B 445 " --> pdb=" O   ASN B 434 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU B 451 " --> pdb=" O   GLU B 464 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU B 464 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   CYS B 453 " --> pdb=" O   SER B 462 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 476
      removed outlier: 3.597A  pdb=" N   SER B 473 " --> pdb=" O   GLY B 486 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 504 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 518
      removed outlier: 6.359A  pdb=" N   VAL B 528 " --> pdb=" O   LEU B 514 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LEU B 516 " --> pdb=" O   ALA B 526 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ALA B 526 " --> pdb=" O   LEU B 516 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   PHE B 518 " --> pdb=" O   TRP B 524 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   TRP B 524 " --> pdb=" O   PHE B 518 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   VAL B 536 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 50
      removed outlier: 3.757A  pdb=" N   MET C  49 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C  75 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.31 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: 3515
        1.34 -     1.46: 1583
        1.46 -     1.58: 6087
        1.58 -     1.70: 0
        1.70 -     1.82: 128
  Bond restraints: 11313
  Sorted by residual:
  bond pdb=" N   VAL B 150 "
       pdb=" CA  VAL B 150 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.17e-02 7.31e+03 8.82e+00
  bond pdb=" CA  ARG A 214 "
       pdb=" CB  ARG A 214 "
    ideal  model  delta    sigma   weight residual
    1.530  1.575 -0.045 1.57e-02 4.06e+03 8.27e+00
  bond pdb=" N   TRP B 151 "
       pdb=" CA  TRP B 151 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.21e-02 6.83e+03 7.19e+00
  bond pdb=" N   GLN B 148 "
       pdb=" CA  GLN B 148 "
    ideal  model  delta    sigma   weight residual
    1.451  1.485 -0.034 1.70e-02 3.46e+03 4.10e+00
  bond pdb=" C   ASP B 146 "
       pdb=" N   PRO B 147 "
    ideal  model  delta    sigma   weight residual
    1.332  1.353 -0.021 1.30e-02 5.92e+03 2.65e+00
  ... (remaining 11308 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.16: 15249
        4.16 -     8.32: 68
        8.32 -    12.48: 2
       12.48 -    16.64: 1
       16.64 -    20.80: 2
  Bond angle restraints: 15322
  Sorted by residual:
  angle pdb=" N   ASP A 854 "
        pdb=" CA  ASP A 854 "
        pdb=" C   ASP A 854 "
      ideal   model   delta    sigma   weight residual
     114.75   93.95   20.80 1.26e+00 6.30e-01 2.72e+02
  angle pdb=" N   ASP A 854 "
        pdb=" CA  ASP A 854 "
        pdb=" CB  ASP A 854 "
      ideal   model   delta    sigma   weight residual
     111.15  127.08  -15.93 1.46e+00 4.69e-01 1.19e+02
  angle pdb=" N   ASP A 853 "
        pdb=" CA  ASP A 853 "
        pdb=" C   ASP A 853 "
      ideal   model   delta    sigma   weight residual
     110.80  128.42  -17.62 2.13e+00 2.20e-01 6.84e+01
  angle pdb=" CA  GLN A 244 "
        pdb=" CB  GLN A 244 "
        pdb=" CG  GLN A 244 "
      ideal   model   delta    sigma   weight residual
     114.10  122.24   -8.14 2.00e+00 2.50e-01 1.65e+01
  angle pdb=" CB  MET A 998 "
        pdb=" CG  MET A 998 "
        pdb=" SD  MET A 998 "
      ideal   model   delta    sigma   weight residual
     112.70  124.34  -11.64 3.00e+00 1.11e-01 1.51e+01
  ... (remaining 15317 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 5780
       17.85 -    35.71: 790
       35.71 -    53.56: 226
       53.56 -    71.42: 37
       71.42 -    89.27: 16
  Dihedral angle restraints: 6849
    sinusoidal: 2750
      harmonic: 4099
  Sorted by residual:
  dihedral pdb=" CA  PRO A 245 "
           pdb=" C   PRO A 245 "
           pdb=" N   ILE A 246 "
           pdb=" CA  ILE A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  MET B 458 "
           pdb=" C   MET B 458 "
           pdb=" N   ALA B 459 "
           pdb=" CA  ALA B 459 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.01   20.99     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" N   ASP A 854 "
           pdb=" C   ASP A 854 "
           pdb=" CA  ASP A 854 "
           pdb=" CB  ASP A 854 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.12   -9.32     0      2.50e+00 1.60e-01 1.39e+01
  ... (remaining 6846 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1702
       0.105 -    0.210: 58
       0.210 -    0.315: 3
       0.315 -    0.420: 0
       0.420 -    0.525: 1
  Chirality restraints: 1764
  Sorted by residual:
  chirality pdb=" CA  ASP A 853 "
            pdb=" N   ASP A 853 "
            pdb=" C   ASP A 853 "
            pdb=" CB  ASP A 853 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" CA  PRO A 212 "
            pdb=" N   PRO A 212 "
            pdb=" C   PRO A 212 "
            pdb=" CB  PRO A 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  PRO B 385 "
            pdb=" N   PRO B 385 "
            pdb=" C   PRO B 385 "
            pdb=" CB  PRO B 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 1761 not shown)

  Planarity restraints: 1939
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 384 "   -0.073 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO B 385 "    0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO B 385 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO B 385 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  43 "   -0.061 5.00e-02 4.00e+02   9.15e-02 1.34e+01
        pdb=" N   PRO C  44 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO C  44 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C  44 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 622 "    0.061 5.00e-02 4.00e+02   9.07e-02 1.32e+01
        pdb=" N   PRO A 623 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO A 623 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 623 "    0.049 5.00e-02 4.00e+02
  ... (remaining 1936 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 468
        2.72 -     3.26: 10546
        3.26 -     3.81: 16543
        3.81 -     4.35: 19028
        4.35 -     4.90: 34061
  Nonbonded interactions: 80646
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 455 "
            pdb=" OE2 GLU A 459 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" O   CYS A 725 "
            pdb=" NH1 ARG A 754 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OE2 GLU B 550 "
            pdb=" OH  TYR B 577 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   SER A 726 "
            pdb=" OG  SER A 726 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR A 351 "
            pdb=" OD2 ASP A 502 "
     model   vdw
     2.232 3.040
  ... (remaining 80641 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
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   0.071  11313  Z= 0.179
  Angle     :  0.813  20.799  15322  Z= 0.440
  Chirality :  0.047   0.525   1764
  Planarity :  0.006   0.112   1939
  Dihedral  : 17.991  89.270   4177
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 29.92 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.23), residues: 1395
  helix:  1.85 (0.24), residues: 499
  sheet: -1.03 (0.32), residues: 274
  loop : -2.23 (0.22), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 255 
 TYR   0.019   0.002   TYR A 856 
 PHE   0.022   0.002   PHE B 557 
 TRP   0.014   0.001   TRP B 525 
 HIS   0.006   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (11313)
  covalent geometry    : angle       0.81263 (15322)
  hydrogen bonds       : bond        0.19403 (  423)
  hydrogen bonds       : angle       6.17250 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 153
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 PHE cc_start: 0.7936 (m-10) cc_final: 0.7582 (m-80)
REVERT: A  225 MET cc_start: 0.7895 (mtt) cc_final: 0.7607 (mtt)
REVERT: A  415 LEU cc_start: 0.7397 (tt) cc_final: 0.6529 (mp)
REVERT: A  499 MET cc_start: 0.7878 (mmt) cc_final: 0.7626 (mmt)
REVERT: A  680 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7283 (mp0)
REVERT: A  744 MET cc_start: 0.7682 (mmt) cc_final: 0.7238 (mmp)
REVERT: B  523 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8489 (mmtm)
  outliers start: 4
  outliers final: 2
  residues processed: 156
  average time/residue: 0.0868
  time to fit residues: 20.0042
Evaluate side-chains
  139 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  854 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    0.0570
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.6302

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 511 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.165799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.128063 restraints weight = 13992.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 3.51
r_work: 0.3690 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11313  Z= 0.107
  Angle     :  0.589   8.249  15322  Z= 0.295
  Chirality :  0.041   0.170   1764
  Planarity :  0.005   0.063   1939
  Dihedral  :  4.395  44.744   1489
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.16 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.23), residues: 1395
  helix:  2.05 (0.24), residues: 511
  sheet: -0.71 (0.32), residues: 281
  loop : -2.06 (0.23), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 174 
 TYR   0.017   0.001   TYR A 856 
 PHE   0.017   0.001   PHE A1005 
 TRP   0.011   0.001   TRP B 525 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11313)
  covalent geometry    : angle       0.58883 (15322)
  hydrogen bonds       : bond        0.03350 (  423)
  hydrogen bonds       : angle       4.30421 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7616 (tmtt)
REVERT: A  177 PHE cc_start: 0.7975 (m-10) cc_final: 0.7697 (m-80)
REVERT: A  211 GLN cc_start: 0.6572 (mm-40) cc_final: 0.6066 (tp-100)
REVERT: A  225 MET cc_start: 0.7945 (mtt) cc_final: 0.7551 (mtt)
REVERT: A  254 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6790 (mp)
REVERT: A  255 ARG cc_start: 0.7925 (mmt90) cc_final: 0.7721 (mmt-90)
REVERT: A  401 MET cc_start: 0.5724 (mtp) cc_final: 0.5449 (mtp)
REVERT: A  717 CYS cc_start: 0.8206 (t) cc_final: 0.7710 (p)
REVERT: A  847 ASN cc_start: 0.7507 (t0) cc_final: 0.7274 (t0)
REVERT: A 1053 ASP cc_start: 0.7735 (p0) cc_final: 0.7400 (p0)
REVERT: B  518 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7553 (t80)
REVERT: C   49 MET cc_start: 0.6962 (ppp) cc_final: 0.6761 (ppp)
  outliers start: 35
  outliers final: 20
  residues processed: 185
  average time/residue: 0.0776
  time to fit residues: 21.4805
Evaluate side-chains
  162 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  106 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 28 optimal weight:    0.6980
   chunk 67 optimal weight:    8.9990
   chunk 54 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.163489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.125929 restraints weight = 14451.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 3.51
r_work: 0.3663 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11313  Z= 0.139
  Angle     :  0.611   8.235  15322  Z= 0.309
  Chirality :  0.042   0.172   1764
  Planarity :  0.004   0.055   1939
  Dihedral  :  4.366  22.656   1485
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 24.16 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.23), residues: 1395
  helix:  1.99 (0.24), residues: 517
  sheet: -0.79 (0.33), residues: 286
  loop : -2.10 (0.23), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.017   0.001   TYR A 856 
 PHE   0.015   0.002   PHE A1005 
 TRP   0.023   0.001   TRP A 202 
 HIS   0.006   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11313)
  covalent geometry    : angle       0.61099 (15322)
  hydrogen bonds       : bond        0.04283 (  423)
  hydrogen bonds       : angle       4.20949 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 143
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.6850 (tpt) cc_final: 0.6611 (tpt)
REVERT: A  177 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7605 (m-80)
REVERT: A  211 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6324 (tp-100)
REVERT: A  225 MET cc_start: 0.8112 (mtt) cc_final: 0.7810 (mtt)
REVERT: A  401 MET cc_start: 0.5954 (mtp) cc_final: 0.5636 (mtp)
REVERT: A  680 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7185 (mp0)
REVERT: A  717 CYS cc_start: 0.8245 (t) cc_final: 0.7718 (p)
REVERT: A 1017 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6656 (mp)
REVERT: A 1046 TRP cc_start: 0.8198 (t60) cc_final: 0.7914 (t60)
REVERT: A 1053 ASP cc_start: 0.7948 (p0) cc_final: 0.7589 (p0)
REVERT: B  387 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7722 (tm-30)
REVERT: B  518 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7613 (t80)
REVERT: C   49 MET cc_start: 0.6950 (ppp) cc_final: 0.6596 (ppp)
REVERT: C   76 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6836 (pt)
  outliers start: 68
  outliers final: 36
  residues processed: 195
  average time/residue: 0.0792
  time to fit residues: 23.7648
Evaluate side-chains
  177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  745 ILE
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1010 SER
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 127 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 133 optimal weight:    5.9990
   chunk 120 optimal weight:    3.9990
   chunk 49 optimal weight:    0.1980
   chunk 109 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.155680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.111934 restraints weight = 13945.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 3.88
r_work: 0.3541 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11313  Z= 0.142
  Angle     :  0.619   9.285  15322  Z= 0.311
  Chirality :  0.042   0.166   1764
  Planarity :  0.004   0.056   1939
  Dihedral  :  4.423  21.806   1485
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 24.72 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.23), residues: 1395
  helix:  1.81 (0.24), residues: 523
  sheet: -0.97 (0.33), residues: 281
  loop : -2.17 (0.22), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.013   0.001   TYR A 856 
 PHE   0.015   0.002   PHE A1005 
 TRP   0.020   0.001   TRP A 202 
 HIS   0.006   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11313)
  covalent geometry    : angle       0.61926 (15322)
  hydrogen bonds       : bond        0.04105 (  423)
  hydrogen bonds       : angle       4.17455 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 136
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.7113 (tpt) cc_final: 0.6849 (tpt)
REVERT: A  211 GLN cc_start: 0.6484 (mm-40) cc_final: 0.6013 (tp-100)
REVERT: A  225 MET cc_start: 0.8127 (mtt) cc_final: 0.7886 (mtt)
REVERT: A  392 MET cc_start: 0.5497 (tmm) cc_final: 0.4802 (tmm)
REVERT: A  401 MET cc_start: 0.5153 (mtp) cc_final: 0.4828 (mtp)
REVERT: A  556 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7316 (tm-30)
REVERT: A  680 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7119 (mp0)
REVERT: A  717 CYS cc_start: 0.8070 (t) cc_final: 0.7537 (p)
REVERT: A 1017 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6268 (mp)
REVERT: A 1046 TRP cc_start: 0.8334 (t60) cc_final: 0.7846 (t60)
REVERT: A 1053 ASP cc_start: 0.7967 (p0) cc_final: 0.7651 (p0)
REVERT: B  518 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7586 (t80)
REVERT: B  523 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8474 (mttt)
REVERT: C   49 MET cc_start: 0.6403 (ppp) cc_final: 0.5995 (ppp)
REVERT: C   76 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6489 (pt)
  outliers start: 68
  outliers final: 47
  residues processed: 191
  average time/residue: 0.0805
  time to fit residues: 23.1772
Evaluate side-chains
  177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 126
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  661 CYS
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  745 ILE
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1010 SER
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 136 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 130 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN
** A 306 ASN ** 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 = 0.4166 r_free = 0.4166 target = 0.154310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.112186 restraints weight = 13662.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 3.77
r_work: 0.3527 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11313  Z= 0.151
  Angle     :  0.618   7.866  15322  Z= 0.315
  Chirality :  0.043   0.193   1764
  Planarity :  0.004   0.058   1939
  Dihedral  :  4.510  22.230   1485
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 24.64 %
    Favored  : 69.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.23), residues: 1395
  helix:  1.77 (0.24), residues: 523
  sheet: -1.03 (0.33), residues: 279
  loop : -2.25 (0.22), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.013   0.001   TYR A 856 
 PHE   0.015   0.002   PHE A 450 
 TRP   0.021   0.001   TRP A 202 
 HIS   0.006   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (11313)
  covalent geometry    : angle       0.61820 (15322)
  hydrogen bonds       : bond        0.04306 (  423)
  hydrogen bonds       : angle       4.20740 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 132
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.7578 (tpt) cc_final: 0.7326 (tpt)
REVERT: A  202 TRP cc_start: 0.7843 (p-90) cc_final: 0.7017 (p90)
REVERT: A  224 ASP cc_start: 0.8464 (p0) cc_final: 0.7998 (p0)
REVERT: A  225 MET cc_start: 0.8262 (mtt) cc_final: 0.7865 (mtp)
REVERT: A  392 MET cc_start: 0.5490 (tmm) cc_final: 0.4788 (tmm)
REVERT: A  401 MET cc_start: 0.5347 (mtp) cc_final: 0.4965 (mtp)
REVERT: A  499 MET cc_start: 0.6610 (mmt) cc_final: 0.6088 (mmm)
REVERT: A  556 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7375 (tm-30)
REVERT: A  680 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7233 (mp0)
REVERT: A 1017 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6343 (mp)
REVERT: B  518 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7603 (t80)
REVERT: C   49 MET cc_start: 0.6388 (ppp) cc_final: 0.5900 (ppp)
REVERT: C   76 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6524 (pt)
  outliers start: 74
  outliers final: 58
  residues processed: 191
  average time/residue: 0.0767
  time to fit residues: 22.0984
Evaluate side-chains
  188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 126
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  661 CYS
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  745 ILE
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  876 MET
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1010 SER
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  313 GLN
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  566 ILE
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 132 optimal weight:    0.9980
   chunk 109 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 136 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 785 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.158347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.119681 restraints weight = 13462.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 4.02
r_work: 0.3571 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6756
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11313  Z= 0.104
  Angle     :  0.578  15.124  15322  Z= 0.285
  Chirality :  0.041   0.171   1764
  Planarity :  0.004   0.055   1939
  Dihedral  :  4.147  21.877   1485
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 27.36 %
    Favored  : 68.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.23), residues: 1395
  helix:  2.07 (0.24), residues: 517
  sheet: -0.92 (0.33), residues: 282
  loop : -2.22 (0.23), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.011   0.001   TYR A 856 
 PHE   0.020   0.001   PHE B 557 
 TRP   0.015   0.001   TRP A 202 
 HIS   0.003   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (11313)
  covalent geometry    : angle       0.57809 (15322)
  hydrogen bonds       : bond        0.03076 (  423)
  hydrogen bonds       : angle       3.86882 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 136
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 TRP cc_start: 0.7788 (p-90) cc_final: 0.6972 (p90)
REVERT: A  224 ASP cc_start: 0.8460 (p0) cc_final: 0.8009 (p0)
REVERT: A  225 MET cc_start: 0.8244 (mtt) cc_final: 0.7997 (mtt)
REVERT: A  234 MET cc_start: 0.8064 (ptp) cc_final: 0.7709 (ppp)
REVERT: A  255 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6876 (mmt-90)
REVERT: A  392 MET cc_start: 0.5506 (tmm) cc_final: 0.4784 (tmm)
REVERT: A  401 MET cc_start: 0.5246 (mtp) cc_final: 0.4887 (mtp)
REVERT: A  427 ASN cc_start: 0.7929 (m110) cc_final: 0.7469 (p0)
REVERT: A  556 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7570 (tm-30)
REVERT: A  680 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7253 (mp0)
REVERT: A  703 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7279 (tt)
REVERT: A 1053 ASP cc_start: 0.7883 (p0) cc_final: 0.7626 (p0)
REVERT: B  330 ASP cc_start: 0.8217 (p0) cc_final: 0.7874 (p0)
REVERT: B  518 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7650 (t80)
REVERT: C   49 MET cc_start: 0.6451 (ppp) cc_final: 0.5943 (ppp)
  outliers start: 52
  outliers final: 34
  residues processed: 177
  average time/residue: 0.0779
  time to fit residues: 20.9634
Evaluate side-chains
  166 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 128
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  861 MET
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0030
   chunk 43 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 115 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 118 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0670
   overall best weight:    0.6730

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 532 GLN
A 982 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.161010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.118523 restraints weight = 13415.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 3.77
r_work: 0.3601 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6643
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11313  Z= 0.100
  Angle     :  0.570  13.883  15322  Z= 0.280
  Chirality :  0.040   0.178   1764
  Planarity :  0.004   0.055   1939
  Dihedral  :  3.983  21.809   1485
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 27.84 %
    Favored  : 68.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.23), residues: 1395
  helix:  2.16 (0.24), residues: 518
  sheet: -0.83 (0.33), residues: 282
  loop : -2.17 (0.23), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.010   0.001   TYR A 856 
 PHE   0.017   0.001   PHE B 557 
 TRP   0.014   0.001   TRP A 202 
 HIS   0.003   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (11313)
  covalent geometry    : angle       0.56991 (15322)
  hydrogen bonds       : bond        0.02853 (  423)
  hydrogen bonds       : angle       3.75456 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 130
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 ASP cc_start: 0.8430 (p0) cc_final: 0.7987 (p0)
REVERT: A  225 MET cc_start: 0.8188 (mtt) cc_final: 0.7976 (mtt)
REVERT: A  234 MET cc_start: 0.8065 (ptp) cc_final: 0.7687 (ppp)
REVERT: A  392 MET cc_start: 0.5345 (tmm) cc_final: 0.4547 (tmm)
REVERT: A  401 MET cc_start: 0.4842 (mtp) cc_final: 0.4573 (mtp)
REVERT: A  427 ASN cc_start: 0.8008 (m110) cc_final: 0.7533 (p0)
REVERT: A  556 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7507 (tm-30)
REVERT: A  680 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7164 (mp0)
REVERT: A  703 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7023 (tt)
REVERT: A 1053 ASP cc_start: 0.7689 (p0) cc_final: 0.7458 (p0)
REVERT: B  172 ASP cc_start: 0.8556 (t0) cc_final: 0.8055 (p0)
REVERT: B  330 ASP cc_start: 0.8108 (p0) cc_final: 0.7739 (p0)
REVERT: C   49 MET cc_start: 0.6280 (ppp) cc_final: 0.5743 (ppp)
REVERT: C  112 HIS cc_start: 0.6366 (m170) cc_final: 0.6141 (m90)
  outliers start: 46
  outliers final: 34
  residues processed: 169
  average time/residue: 0.0778
  time to fit residues: 20.2608
Evaluate side-chains
  158 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  313 GLN
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 116 optimal weight:    0.0370
   chunk 126 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 130 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.1262

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.157531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.113545 restraints weight = 13751.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 3.93
r_work: 0.3551 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11313  Z= 0.113
  Angle     :  0.587  13.237  15322  Z= 0.291
  Chirality :  0.041   0.189   1764
  Planarity :  0.004   0.055   1939
  Dihedral  :  4.047  21.462   1485
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 27.52 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.23), residues: 1395
  helix:  2.12 (0.24), residues: 517
  sheet: -0.88 (0.32), residues: 287
  loop : -2.16 (0.23), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.010   0.001   TYR A 856 
 PHE   0.016   0.001   PHE B 557 
 TRP   0.024   0.001   TRP A 202 
 HIS   0.004   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (11313)
  covalent geometry    : angle       0.58658 (15322)
  hydrogen bonds       : bond        0.03334 (  423)
  hydrogen bonds       : angle       3.78696 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 120
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 ASP cc_start: 0.8433 (p0) cc_final: 0.7992 (p0)
REVERT: A  225 MET cc_start: 0.8227 (mtt) cc_final: 0.8000 (mtt)
REVERT: A  234 MET cc_start: 0.8138 (ptp) cc_final: 0.7607 (ppp)
REVERT: A  392 MET cc_start: 0.5258 (tmm) cc_final: 0.4532 (tmm)
REVERT: A  401 MET cc_start: 0.5004 (mtp) cc_final: 0.4699 (mtp)
REVERT: A  427 ASN cc_start: 0.8049 (m110) cc_final: 0.7539 (p0)
REVERT: A  556 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7519 (tm-30)
REVERT: A  680 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7234 (mp0)
REVERT: A  703 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7086 (tt)
REVERT: B  172 ASP cc_start: 0.8599 (t0) cc_final: 0.8145 (p0)
REVERT: B  330 ASP cc_start: 0.8092 (p0) cc_final: 0.7764 (p0)
REVERT: B  387 GLU cc_start: 0.8677 (mp0) cc_final: 0.8461 (pt0)
REVERT: B  518 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7631 (t80)
REVERT: C   49 MET cc_start: 0.6283 (ppp) cc_final: 0.5097 (ppp)
REVERT: C  112 HIS cc_start: 0.6295 (m170) cc_final: 0.6055 (m90)
  outliers start: 54
  outliers final: 45
  residues processed: 163
  average time/residue: 0.0750
  time to fit residues: 19.4190
Evaluate side-chains
  162 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 114
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  661 CYS
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  861 MET
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  313 GLN
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  105 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 79 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0370
   chunk 34 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 115 optimal weight:   10.0000
   chunk 120 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    2.0064

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 HIS
A 532 GLN
** A 763 ASN ** 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 = 0.4143 r_free = 0.4143 target = 0.154269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.110741 restraints weight = 13715.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 3.77
r_work: 0.3494 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11313  Z= 0.153
  Angle     :  0.634  12.957  15322  Z= 0.319
  Chirality :  0.043   0.177   1764
  Planarity :  0.004   0.057   1939
  Dihedral  :  4.470  21.714   1485
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.28 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.23), residues: 1395
  helix:  1.91 (0.24), residues: 517
  sheet: -1.03 (0.32), residues: 284
  loop : -2.28 (0.23), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.012   0.001   TYR A 700 
 PHE   0.016   0.002   PHE B 557 
 TRP   0.020   0.001   TRP A 202 
 HIS   0.006   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (11313)
  covalent geometry    : angle       0.63404 (15322)
  hydrogen bonds       : bond        0.04340 (  423)
  hydrogen bonds       : angle       4.05273 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 117
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 TRP cc_start: 0.7859 (p-90) cc_final: 0.6708 (p90)
REVERT: A  224 ASP cc_start: 0.8481 (p0) cc_final: 0.8034 (p0)
REVERT: A  225 MET cc_start: 0.8297 (mtt) cc_final: 0.7603 (mtp)
REVERT: A  234 MET cc_start: 0.8089 (ptp) cc_final: 0.7600 (ppp)
REVERT: A  392 MET cc_start: 0.5474 (tmm) cc_final: 0.4720 (tmm)
REVERT: A  401 MET cc_start: 0.5234 (mtp) cc_final: 0.4906 (mtp)
REVERT: A  427 ASN cc_start: 0.8046 (m110) cc_final: 0.7566 (p0)
REVERT: A  556 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7387 (tm-30)
REVERT: A  680 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7307 (mp0)
REVERT: A  703 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7136 (tt)
REVERT: B  330 ASP cc_start: 0.8139 (p0) cc_final: 0.7799 (p0)
REVERT: B  518 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7639 (t80)
REVERT: C   49 MET cc_start: 0.6385 (ppp) cc_final: 0.5147 (ppp)
REVERT: C  112 HIS cc_start: 0.6466 (m170) cc_final: 0.6237 (m90)
  outliers start: 57
  outliers final: 49
  residues processed: 164
  average time/residue: 0.0783
  time to fit residues: 20.4601
Evaluate side-chains
  167 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 HIS
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  661 CYS
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  313 GLN
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  575 SER
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   90 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 115 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 134 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0000
   chunk 32 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 97 optimal weight:    0.0670
   overall best weight:    0.5322

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 532 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.160453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.116137 restraints weight = 13463.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 3.86
r_work: 0.3564 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11313  Z= 0.098
  Angle     :  0.571  12.737  15322  Z= 0.283
  Chirality :  0.040   0.169   1764
  Planarity :  0.004   0.055   1939
  Dihedral  :  4.034  21.769   1485
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 28.96 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.23), residues: 1395
  helix:  2.13 (0.24), residues: 517
  sheet: -0.80 (0.33), residues: 277
  loop : -2.19 (0.23), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 349 
 TYR   0.011   0.001   TYR A 856 
 PHE   0.017   0.001   PHE B 557 
 TRP   0.021   0.001   TRP A 202 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (11313)
  covalent geometry    : angle       0.57115 (15322)
  hydrogen bonds       : bond        0.02741 (  423)
  hydrogen bonds       : angle       3.70152 ( 1227)

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

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

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2790 Ramachandran restraints generated.
    1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 TRP cc_start: 0.7806 (p-90) cc_final: 0.6671 (p90)
REVERT: A  224 ASP cc_start: 0.8458 (p0) cc_final: 0.8008 (p0)
REVERT: A  225 MET cc_start: 0.8244 (mtt) cc_final: 0.7563 (mtp)
REVERT: A  234 MET cc_start: 0.7982 (ptp) cc_final: 0.7493 (ppp)
REVERT: A  392 MET cc_start: 0.5437 (tmm) cc_final: 0.4686 (tmm)
REVERT: A  401 MET cc_start: 0.4887 (mtp) cc_final: 0.4654 (mtp)
REVERT: A  427 ASN cc_start: 0.8145 (m110) cc_final: 0.7673 (p0)
REVERT: A  556 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7551 (tm-30)
REVERT: A  680 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7296 (mp0)
REVERT: A  703 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7128 (tt)
REVERT: A  829 GLN cc_start: 0.8631 (tp40) cc_final: 0.8415 (tt0)
REVERT: A  980 ASN cc_start: 0.7965 (t0) cc_final: 0.7640 (t0)
REVERT: B  172 ASP cc_start: 0.8515 (t0) cc_final: 0.8061 (p0)
REVERT: B  330 ASP cc_start: 0.8112 (p0) cc_final: 0.7816 (p0)
REVERT: B  518 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7557 (t80)
REVERT: C   49 MET cc_start: 0.6378 (ppp) cc_final: 0.5821 (ppp)
REVERT: C  112 HIS cc_start: 0.6490 (m170) cc_final: 0.6273 (m90)
  outliers start: 36
  outliers final: 32
  residues processed: 156
  average time/residue: 0.0826
  time to fit residues: 20.2017
Evaluate side-chains
  153 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  836 ASN
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue  974 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  386 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  518 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   52 TRP
Chi-restraints excluded: chain C residue   90 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0770
   chunk 130 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.157252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.116459 restraints weight = 13749.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 3.88
r_work: 0.3531 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11313  Z= 0.121
  Angle     :  0.601  12.852  15322  Z= 0.299
  Chirality :  0.041   0.167   1764
  Planarity :  0.004   0.056   1939
  Dihedral  :  4.125  21.355   1485
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 28.32 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.23), residues: 1395
  helix:  2.04 (0.24), residues: 517
  sheet: -0.97 (0.32), residues: 285
  loop : -2.23 (0.23), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 349 
 TYR   0.009   0.001   TYR A 856 
 PHE   0.016   0.001   PHE B 557 
 TRP   0.019   0.001   TRP A 202 
 HIS   0.004   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (11313)
  covalent geometry    : angle       0.60091 (15322)
  hydrogen bonds       : bond        0.03500 (  423)
  hydrogen bonds       : angle       3.81527 ( 1227)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2271.61 seconds
wall clock time: 39 minutes 45.06 seconds (2385.06 seconds total)