Starting phenix.real_space_refine
on Fri Feb 14 14:43:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c60_16449/02_2025/8c60_16449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c60_16449/02_2025/8c60_16449.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c60_16449/02_2025/8c60_16449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c60_16449/02_2025/8c60_16449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c60_16449/02_2025/8c60_16449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c60_16449/02_2025/8c60_16449.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      5      6.06       5
     S      71      5.16       5
     C    6618      2.51       5
     N    1791      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10393
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4403
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 518}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 2956
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 368, 2956
          Classifications: {'peptide': 368}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 1692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1692
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 191}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1335
          Classifications: {'peptide': 163}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 153}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8431  SG  CYS C 289      37.156  60.679  44.363  1.00 98.27           S
  ATOM   8457  SG  CYS C 292      34.484  59.125  42.002  1.00 76.90           S
  ATOM   8640  SG  CYS C 315      38.214  58.340  41.438  1.00 99.87           S
  ATOM   8315  SG  CYS C 274      37.578  47.560  46.382  1.00 76.54           S
  ATOM   8339  SG  CYS C 277      38.854  43.874  45.997  1.00 76.10           S
  ATOM   8523  SG  CYS C 300      41.127  46.197  47.023  1.00 52.30           S
  ATOM   7590  SG  CYS C  71      45.057  96.067  75.745  1.00157.09           S
  ATOM   7614  SG  CYS C  74      42.007  94.820  73.799  1.00171.24           S
  ATOM   7806  SG  CYS C  99      44.586  97.004  72.093  1.00151.70           S
  ATOM   7833  SG  CYS C 102      42.314  98.532  74.632  1.00154.53           S
  ATOM   7508  SG  CYS C  59      47.178  87.777  66.516  1.00171.80           S
  ATOM   7528  SG  CYS C  62      47.624  85.720  63.345  1.00149.40           S
  ATOM   7675  SG  CYS C  82      49.675  88.925  63.768  1.00152.27           S

  Time building chain proxies: 5.87, per 1000 atoms: 0.56
  Number of scatterers: 10393
  At special positions: 0
  Unit cell: (121.338, 127.008, 108.864, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      5     29.99
     Ca      2     19.99
     S      71     16.00
     O    1906      8.00
     N    1791      7.00
     C    6618      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: 2.60
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" NE2 HIS B 179 "
      pdb="  ZN C1101 "
        pdb="ZN    ZN C1101 " - pdb=" NE2 HIS C 318 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 315 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 292 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 289 "
      pdb="  ZN C1102 "
        pdb="ZN    ZN C1102 " - pdb=" ND1 HIS C 297 "
        pdb="ZN    ZN C1102 " - pdb=" SG  CYS C 300 "
        pdb="ZN    ZN C1102 " - pdb=" SG  CYS C 277 "
        pdb="ZN    ZN C1102 " - pdb=" SG  CYS C 274 "
      pdb="  ZN C1103 "
        pdb="ZN    ZN C1103 " - pdb=" SG  CYS C  99 "
        pdb="ZN    ZN C1103 " - pdb=" SG  CYS C 102 "
        pdb="ZN    ZN C1103 " - pdb=" SG  CYS C  74 "
        pdb="ZN    ZN C1103 " - pdb=" SG  CYS C  71 "
      pdb="  ZN C1104 "
        pdb="ZN    ZN C1104 " - pdb=" ND1 HIS C  79 "
        pdb="ZN    ZN C1104 " - pdb=" SG  CYS C  62 "
        pdb="ZN    ZN C1104 " - pdb=" SG  CYS C  59 "
        pdb="ZN    ZN C1104 " - pdb=" SG  CYS C  82 "
      Number of angles added : 15


  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2434

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 5 sheets defined
      59.4% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 304 through 319
      removed outlier: 3.722A  pdb=" N   PHE A 308 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS A 319 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 336
    Processing helix  chain 'A' and resid 340 through 353
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 355 through 367
    Processing helix  chain 'A' and resid 417 through 424
    Processing helix  chain 'A' and resid 446 through 484
      removed outlier: 3.673A  pdb=" N   GLU A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLN A 451 " --> pdb=" O   PRO A 447 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 452 " --> pdb=" O   TYR A 448 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 492
      removed outlier: 4.088A  pdb=" N   GLU A 492 " --> pdb=" O   PRO A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 517
    Processing helix  chain 'A' and resid 519 through 530
    Processing helix  chain 'A' and resid 530 through 561
      Proline residue:  A 536  - end of helix
    Processing helix  chain 'A' and resid 567 through 573
    Processing helix  chain 'A' and resid 575 through 587
      removed outlier: 3.916A  pdb=" N   GLN A 581 " --> pdb=" O   VAL A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 610
      removed outlier: 3.527A  pdb=" N   ILE A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL A 599 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 642
    Processing helix  chain 'A' and resid 648 through 661
    Processing helix  chain 'A' and resid 661 through 667
    Processing helix  chain 'A' and resid 746 through 786
      removed outlier: 3.711A  pdb=" N   LEU A 786 " --> pdb=" O   GLU A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 792
      removed outlier: 3.537A  pdb=" N   ARG A 792 " --> pdb=" O   GLU A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 814
    Processing helix  chain 'A' and resid 814 through 829
    Processing helix  chain 'A' and resid 832 through 845
    Processing helix  chain 'A' and resid 846 through 852
      removed outlier: 4.348A  pdb=" N   TYR A 849 " --> pdb=" O   ILE A 846 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 850 " --> pdb=" O   HIS A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 871
      removed outlier: 3.518A  pdb=" N   LEU A 857 " --> pdb=" O   THR A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 888
      removed outlier: 3.662A  pdb=" N   LEU A 875 " --> pdb=" O   ASP A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 913
      removed outlier: 5.169A  pdb=" N   ALA A 902 " --> pdb=" O   CYS A 898 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ARG A 903 " --> pdb=" O   VAL A 899 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 23
    Processing helix  chain 'B' and resid 33 through 46
      removed outlier: 4.044A  pdb=" N   ARG B  37 " --> pdb=" O   PRO B  33 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   MET B  38 " --> pdb=" O   HIS B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 70 through 80
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 4.072A  pdb=" N   MET B  85 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 95
    Processing helix  chain 'B' and resid 106 through 127
      removed outlier: 3.576A  pdb=" N   SER B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 165
      removed outlier: 3.501A  pdb=" N   LEU B 159 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 188
    Processing helix  chain 'B' and resid 217 through 221
    Processing helix  chain 'B' and resid 234 through 254
      removed outlier: 3.508A  pdb=" N   LYS B 243 " --> pdb=" O   GLY B 239 " (cutoff:3.500A)
      Proline residue:  B 244  - end of helix
    Processing helix  chain 'B' and resid 263 through 267
      removed outlier: 4.038A  pdb=" N   SER B 266 " --> pdb=" O   GLY B 263 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU B 267 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 263 through 267'
    Processing helix  chain 'B' and resid 278 through 291
      removed outlier: 3.952A  pdb=" N   CYS B 285 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL B 286 " --> pdb=" O   HIS B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 321
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.683A  pdb=" N   GLY B 339 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 373
      removed outlier: 3.854A  pdb=" N   MET B 373 " --> pdb=" O   GLU B 369 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 29
      removed outlier: 3.513A  pdb=" N   ILE C  24 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 112
    Processing helix  chain 'C' and resid 206 through 220
    Processing helix  chain 'C' and resid 228 through 233
      removed outlier: 3.510A  pdb=" N   CYS C 233 " --> pdb=" O   ASN C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 325
      removed outlier: 4.061A  pdb=" N   VAL C 323 " --> pdb=" O   ILE C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 341
      removed outlier: 3.605A  pdb=" N   ARG C 334 " --> pdb=" O   THR C 330 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE C 341 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 360
    Processing helix  chain 'D' and resid 205 through 216
      removed outlier: 3.786A  pdb=" N   ASP D 209 " --> pdb=" O   PRO D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 241
    Processing helix  chain 'D' and resid 249 through 266
      removed outlier: 4.339A  pdb=" N   GLU D 255 " --> pdb=" O   TYR D 251 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL D 266 " --> pdb=" O   GLU D 262 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 288
    Processing helix  chain 'D' and resid 298 through 313
      removed outlier: 3.925A  pdb=" N   LEU D 302 " --> pdb=" O   GLY D 298 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU D 303 " --> pdb=" O   ALA D 299 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ARG D 304 " --> pdb=" O   PRO D 300 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU D 305 " --> pdb=" O   HIS D 301 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE D 306 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY D 310 " --> pdb=" O   PHE D 306 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ALA D 311 " --> pdb=" O   VAL D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 314 through 316
      No H-bonds generated for 'chain 'D' and resid 314 through 316'
    Processing helix  chain 'D' and resid 319 through 340
    Processing helix  chain 'D' and resid 340 through 345
    Processing helix  chain 'D' and resid 354 through 362
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397
      removed outlier: 3.741A  pdb=" N   ILE A 397 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   TYR A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624
      removed outlier: 4.030A  pdb=" N   VAL A 739 " --> pdb=" O   GLN A 927 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55
      removed outlier: 6.732A  pdb=" N   TYR B  14 " --> pdb=" O   TYR B  55 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ALA B 133 " --> pdb=" O   MET B 298 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 258 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   LEU B 299 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU B 260 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   GLN B 261 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE B 174 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 171 " --> pdb=" O   MET B 195 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   VAL B 197 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   TYR B 173 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   PHE B 199 " --> pdb=" O   TYR B 173 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B 175 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 8.549A  pdb=" N   LYS B 201 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 70
    Processing sheet with id=AA5, first strand: chain 'C' and resid 287 through 288

    523 hydrogen bonds defined for protein.
    1521 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 3.04 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: 3402
        1.34 -     1.46: 2277
        1.46 -     1.58: 4842
        1.58 -     1.70: 2
        1.70 -     1.82: 104
  Bond restraints: 10627
  Sorted by residual:
  bond pdb=" CG  LEU A 753 "
       pdb=" CD2 LEU A 753 "
    ideal  model  delta    sigma   weight residual
    1.521  1.448  0.073 3.30e-02 9.18e+02 4.84e+00
  bond pdb=" C   LYS D 204 "
       pdb=" N   PRO D 205 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.24e+00
  bond pdb=" CB  PRO A 664 "
       pdb=" CG  PRO A 664 "
    ideal  model  delta    sigma   weight residual
    1.492  1.588 -0.096 5.00e-02 4.00e+02 3.69e+00
  bond pdb=" CB  PRO C 293 "
       pdb=" CG  PRO C 293 "
    ideal  model  delta    sigma   weight residual
    1.492  1.586 -0.094 5.00e-02 4.00e+02 3.51e+00
  bond pdb=" C   ALA D 299 "
       pdb=" N   PRO D 300 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.44e-02 4.82e+03 3.14e+00
  ... (remaining 10622 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 14224
        3.26 -     6.51: 107
        6.51 -     9.77: 17
        9.77 -    13.02: 3
       13.02 -    16.28: 1
  Bond angle restraints: 14352
  Sorted by residual:
  angle pdb=" CA  PRO A 664 "
        pdb=" N   PRO A 664 "
        pdb=" CD  PRO A 664 "
      ideal   model   delta    sigma   weight residual
     112.00  104.30    7.70 1.40e+00 5.10e-01 3.03e+01
  angle pdb=" CA  LEU A 347 "
        pdb=" CB  LEU A 347 "
        pdb=" CG  LEU A 347 "
      ideal   model   delta    sigma   weight residual
     116.30  132.58  -16.28 3.50e+00 8.16e-02 2.16e+01
  angle pdb=" C   GLY D 298 "
        pdb=" N   ALA D 299 "
        pdb=" CA  ALA D 299 "
      ideal   model   delta    sigma   weight residual
     120.09  125.59   -5.50 1.25e+00 6.40e-01 1.94e+01
  angle pdb=" CA  PRO C 293 "
        pdb=" N   PRO C 293 "
        pdb=" CD  PRO C 293 "
      ideal   model   delta    sigma   weight residual
     112.00  106.52    5.48 1.40e+00 5.10e-01 1.53e+01
  angle pdb=" CG  MET A 934 "
        pdb=" SD  MET A 934 "
        pdb=" CE  MET A 934 "
      ideal   model   delta    sigma   weight residual
     100.90   92.53    8.37 2.20e+00 2.07e-01 1.45e+01
  ... (remaining 14347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 5443
       17.29 -    34.59: 701
       34.59 -    51.88: 248
       51.88 -    69.18: 40
       69.18 -    86.47: 17
  Dihedral angle restraints: 6449
    sinusoidal: 2681
      harmonic: 3768
  Sorted by residual:
  dihedral pdb=" CA  THR B 305 "
           pdb=" C   THR B 305 "
           pdb=" N   ILE B 306 "
           pdb=" CA  ILE B 306 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.50  -22.50     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  LYS C 272 "
           pdb=" C   LYS C 272 "
           pdb=" N   VAL C 273 "
           pdb=" CA  VAL C 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  TYR B  16 "
           pdb=" C   TYR B  16 "
           pdb=" N   ASP B  17 "
           pdb=" CA  ASP B  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.43   19.57     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 6446 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1498
       0.107 -    0.215: 33
       0.215 -    0.322: 1
       0.322 -    0.429: 1
       0.429 -    0.537: 1
  Chirality restraints: 1534
  Sorted by residual:
  chirality pdb=" CG  LEU C 213 "
            pdb=" CB  LEU C 213 "
            pdb=" CD1 LEU C 213 "
            pdb=" CD2 LEU C 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.05   -0.54 2.00e-01 2.50e+01 7.20e+00
  chirality pdb=" CG  LEU C 355 "
            pdb=" CB  LEU C 355 "
            pdb=" CD1 LEU C 355 "
            pdb=" CD2 LEU C 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CG  LEU D 213 "
            pdb=" CB  LEU D 213 "
            pdb=" CD1 LEU D 213 "
            pdb=" CD2 LEU D 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.15e+00
  ... (remaining 1531 not shown)

  Planarity restraints: 1862
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 663 "    0.079 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO A 664 "   -0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO A 664 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A 664 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 292 "   -0.054 5.00e-02 4.00e+02   7.84e-02 9.83e+00
        pdb=" N   PRO C 293 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO C 293 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 293 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 315 "   -0.198 9.50e-02 1.11e+02   8.93e-02 6.15e+00
        pdb=" NE  ARG A 315 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 315 "    0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 315 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 315 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1859 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 33
        2.38 -     3.01: 5937
        3.01 -     3.64: 16128
        3.64 -     4.27: 23576
        4.27 -     4.90: 39100
  Nonbonded interactions: 84774
  Sorted by model distance:
  nonbonded pdb=" CG  HIS B 179 "
            pdb="ZN    ZN B 501 "
     model   vdw
     1.750 1.960
  nonbonded pdb=" OD1 ASP B 177 "
            pdb="ZN    ZN B 501 "
     model   vdw
     2.136 2.230
  nonbonded pdb=" ND2 ASN B  96 "
            pdb=" O   ALA B 148 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OG1 THR C 330 "
            pdb=" OD1 ASN C 333 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ASN D 228 "
            pdb=" OG  SER D 231 "
     model   vdw
     2.265 3.040
  ... (remaining 84769 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.150
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
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   0.096  10627  Z= 0.249
  Angle     :  0.783  16.276  14352  Z= 0.404
  Chirality :  0.047   0.537   1534
  Planarity :  0.006   0.114   1862
  Dihedral  : 17.712  86.471   4015
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 29.15 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.24), residues: 1260
  helix:  0.70 (0.20), residues: 671
  sheet: -0.50 (0.63), residues: 74
  loop : -0.95 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 560 
 HIS   0.004   0.001   HIS C 297 
 PHE   0.031   0.002   PHE A 743 
 TYR   0.036   0.002   TYR D 236 
 ARG   0.020   0.001   ARG A 315 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 279
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 LYS cc_start: 0.7588 (tptt) cc_final: 0.7081 (tptm)
REVERT: A  557 ASN cc_start: 0.7745 (t0) cc_final: 0.7510 (t0)
REVERT: A  570 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8063 (ttpp)
REVERT: A  625 GLU cc_start: 0.6413 (pm20) cc_final: 0.5180 (pm20)
REVERT: A  771 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7604 (mt0)
REVERT: A  776 GLU cc_start: 0.7120 (tp30) cc_final: 0.6705 (tp30)
REVERT: A  822 MET cc_start: 0.7800 (ttm) cc_final: 0.7546 (ttm)
REVERT: A  843 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7546 (mpp)
REVERT: A  922 LYS cc_start: 0.8008 (tmmt) cc_final: 0.7782 (tmmt)
REVERT: B   75 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7247 (mmmt)
REVERT: B  265 ASP cc_start: 0.6929 (p0) cc_final: 0.6626 (p0)
  outliers start: 9
  outliers final: 1
  residues processed: 281
  average time/residue: 0.2644
  time to fit residues: 99.3864
Evaluate side-chains
  272 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 270
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  843 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.3980
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 64 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 98 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 73 optimal weight:    0.1980
   chunk 114 optimal weight:   10.0000
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
A 557 ASN
A 574 HIS
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 859 GLN
** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 HIS
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.179218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.152015 restraints weight = 16454.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.77
r_work: 0.3795 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10627  Z= 0.188
  Angle     :  0.632  12.570  14352  Z= 0.315
  Chirality :  0.043   0.296   1534
  Planarity :  0.005   0.066   1862
  Dihedral  :  4.304  24.607   1413
  Min Nonbonded Distance : 1.769

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.82 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.24), residues: 1260
  helix:  1.24 (0.20), residues: 671
  sheet: -0.41 (0.63), residues: 74
  loop : -0.87 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 560 
 HIS   0.008   0.001   HIS B  58 
 PHE   0.027   0.002   PHE A 743 
 TYR   0.027   0.002   TYR D 329 
 ARG   0.006   0.000   ARG A 762 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 279
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 ASP cc_start: 0.7282 (m-30) cc_final: 0.7052 (m-30)
REVERT: A  503 THR cc_start: 0.7841 (p) cc_final: 0.7489 (m)
REVERT: A  540 LYS cc_start: 0.7630 (mttp) cc_final: 0.7406 (mttp)
REVERT: A  545 LYS cc_start: 0.7519 (tptt) cc_final: 0.7012 (tptm)
REVERT: A  557 ASN cc_start: 0.7680 (t160) cc_final: 0.7438 (t0)
REVERT: A  570 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7705 (ttpp)
REVERT: A  741 SER cc_start: 0.8079 (t) cc_final: 0.7521 (p)
REVERT: A  787 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.4045 (tt)
REVERT: A  814 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6368 (mt-10)
REVERT: A  835 GLN cc_start: 0.7391 (mp10) cc_final: 0.7175 (mp10)
REVERT: A  922 LYS cc_start: 0.8080 (tmmt) cc_final: 0.7705 (tptt)
REVERT: B   44 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5871 (mp)
REVERT: B   75 LYS cc_start: 0.7590 (mmmt) cc_final: 0.7338 (mmmt)
REVERT: B  127 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7032 (mpp80)
REVERT: B  131 ASP cc_start: 0.6588 (p0) cc_final: 0.6374 (p0)
REVERT: B  151 PHE cc_start: 0.8517 (m-10) cc_final: 0.8076 (m-80)
REVERT: B  185 GLU cc_start: 0.7349 (tt0) cc_final: 0.7063 (tt0)
REVERT: B  243 LYS cc_start: 0.7920 (tttp) cc_final: 0.7682 (ttpt)
REVERT: B  336 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7235 (mm-30)
REVERT: C   20 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7301 (tt)
REVERT: C  298 MET cc_start: 0.8021 (mmm) cc_final: 0.7790 (mmt)
REVERT: C  305 LEU cc_start: 0.8145 (mt) cc_final: 0.7865 (mp)
  outliers start: 37
  outliers final: 15
  residues processed: 293
  average time/residue: 0.2954
  time to fit residues: 114.8108
Evaluate side-chains
  272 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 253
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  871 ASP
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  147 GLU
Chi-restraints excluded: chain B residue  195 MET
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  272 LYS
Chi-restraints excluded: chain C residue  282 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 4 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 619 HIS
A 773 GLN
A 867 HIS
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 228 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.172824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144885 restraints weight = 16140.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 2.72
r_work: 0.3695 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10627  Z= 0.249
  Angle     :  0.637  13.465  14352  Z= 0.316
  Chirality :  0.043   0.218   1534
  Planarity :  0.004   0.049   1862
  Dihedral  :  4.183  22.264   1408
  Min Nonbonded Distance : 1.710

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 25.62 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1260
  helix:  1.32 (0.20), residues: 675
  sheet: -0.44 (0.63), residues: 75
  loop : -0.85 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 560 
 HIS   0.005   0.001   HIS C 297 
 PHE   0.016   0.002   PHE A 751 
 TYR   0.023   0.002   TYR D 329 
 ARG   0.007   0.001   ARG A 768 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 294
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 TYR cc_start: 0.7466 (m-80) cc_final: 0.7181 (m-10)
REVERT: A  444 LYS cc_start: 0.5249 (mttt) cc_final: 0.3826 (ptpt)
REVERT: A  457 ASP cc_start: 0.7518 (m-30) cc_final: 0.7151 (m-30)
REVERT: A  458 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7122 (mt-10)
REVERT: A  470 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8076 (mm)
REVERT: A  475 VAL cc_start: 0.7918 (t) cc_final: 0.7682 (p)
REVERT: A  522 GLU cc_start: 0.7363 (mp0) cc_final: 0.7065 (mp0)
REVERT: A  546 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6847 (tm-30)
REVERT: A  601 ASP cc_start: 0.6822 (m-30) cc_final: 0.6558 (m-30)
REVERT: A  787 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4200 (tt)
REVERT: A  814 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6599 (mt-10)
REVERT: A  822 MET cc_start: 0.7909 (ttm) cc_final: 0.7707 (ttm)
REVERT: A  835 GLN cc_start: 0.7507 (mp10) cc_final: 0.7195 (mp10)
REVERT: A  857 LEU cc_start: 0.7685 (tp) cc_final: 0.7391 (tp)
REVERT: A  936 ILE cc_start: 0.8097 (pt) cc_final: 0.7741 (mt)
REVERT: B   75 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7350 (mtmm)
REVERT: B   91 GLN cc_start: 0.8234 (mt0) cc_final: 0.8006 (mt0)
REVERT: B  127 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7250 (mpp80)
REVERT: B  131 ASP cc_start: 0.6817 (p0) cc_final: 0.6584 (p0)
REVERT: B  151 PHE cc_start: 0.8578 (m-10) cc_final: 0.8115 (m-80)
REVERT: B  155 ASN cc_start: 0.8219 (t0) cc_final: 0.7925 (t0)
REVERT: B  185 GLU cc_start: 0.7670 (tt0) cc_final: 0.7469 (tt0)
REVERT: B  211 ASP cc_start: 0.7085 (m-30) cc_final: 0.6829 (t0)
REVERT: B  336 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7193 (mm-30)
REVERT: B  360 MET cc_start: 0.7899 (mmt) cc_final: 0.7458 (mmm)
REVERT: C   91 MET cc_start: 0.5318 (tpt) cc_final: 0.5090 (tpt)
REVERT: C  286 LEU cc_start: 0.8362 (mt) cc_final: 0.8098 (mm)
REVERT: D  206 TRP cc_start: 0.8541 (t-100) cc_final: 0.8308 (t-100)
REVERT: D  261 LYS cc_start: 0.8153 (mttm) cc_final: 0.7916 (mttm)
REVERT: D  265 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6743 (m110)
  outliers start: 35
  outliers final: 18
  residues processed: 311
  average time/residue: 0.2966
  time to fit residues: 122.4982
Evaluate side-chains
  287 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 265
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  871 ASP
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  147 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain D residue  265 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   chunk 115 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 91 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 480 GLN
A 557 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.168278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.140559 restraints weight = 16116.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.50
r_work: 0.3643 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10627  Z= 0.303
  Angle     :  0.658  13.274  14352  Z= 0.329
  Chirality :  0.045   0.227   1534
  Planarity :  0.004   0.057   1862
  Dihedral  :  4.254  22.813   1408
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 25.71 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1260
  helix:  1.14 (0.20), residues: 681
  sheet: -0.40 (0.63), residues: 74
  loop : -0.90 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 560 
 HIS   0.005   0.001   HIS C 318 
 PHE   0.021   0.002   PHE A 362 
 TYR   0.025   0.002   TYR D 329 
 ARG   0.010   0.001   ARG A 315 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 296
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 ARG cc_start: 0.6842 (mmp80) cc_final: 0.6508 (mmp-170)
REVERT: A  322 GLU cc_start: 0.6907 (pm20) cc_final: 0.6637 (pm20)
REVERT: A  428 TRP cc_start: 0.8566 (m100) cc_final: 0.7909 (m100)
REVERT: A  457 ASP cc_start: 0.7517 (m-30) cc_final: 0.7032 (m-30)
REVERT: A  458 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7094 (mt-10)
REVERT: A  463 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7212 (t0)
REVERT: A  470 LEU cc_start: 0.8543 (mp) cc_final: 0.8277 (mm)
REVERT: A  519 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7402 (mtmm)
REVERT: A  522 GLU cc_start: 0.7403 (mp0) cc_final: 0.7169 (mp0)
REVERT: A  559 ILE cc_start: 0.7491 (mt) cc_final: 0.7120 (mt)
REVERT: A  580 LYS cc_start: 0.8334 (mmmm) cc_final: 0.7738 (mtmm)
REVERT: A  597 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: A  601 ASP cc_start: 0.6970 (m-30) cc_final: 0.6711 (m-30)
REVERT: A  625 GLU cc_start: 0.6843 (pm20) cc_final: 0.5553 (mt-10)
REVERT: A  643 ARG cc_start: 0.6846 (mtt-85) cc_final: 0.6564 (mtt-85)
REVERT: A  741 SER cc_start: 0.8307 (t) cc_final: 0.7627 (p)
REVERT: A  746 ASN cc_start: 0.8375 (p0) cc_final: 0.8154 (p0)
REVERT: A  776 GLU cc_start: 0.7387 (tp30) cc_final: 0.7015 (tp30)
REVERT: A  787 LEU cc_start: 0.4431 (OUTLIER) cc_final: 0.4208 (tt)
REVERT: A  822 MET cc_start: 0.7863 (ttm) cc_final: 0.7547 (ttm)
REVERT: A  835 GLN cc_start: 0.7457 (mp10) cc_final: 0.7181 (mp10)
REVERT: A  855 ASP cc_start: 0.7335 (p0) cc_final: 0.7062 (p0)
REVERT: A  922 LYS cc_start: 0.8193 (tmmt) cc_final: 0.7759 (tptm)
REVERT: A  935 THR cc_start: 0.8323 (m) cc_final: 0.7596 (p)
REVERT: B   44 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6374 (mp)
REVERT: B   49 TYR cc_start: 0.6508 (p90) cc_final: 0.6258 (p90)
REVERT: B   74 ILE cc_start: 0.7577 (mm) cc_final: 0.7229 (mm)
REVERT: B   75 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7436 (mtmm)
REVERT: B   91 GLN cc_start: 0.8205 (mt0) cc_final: 0.7971 (mt0)
REVERT: B   92 MET cc_start: 0.8528 (ttt) cc_final: 0.8190 (ttm)
REVERT: B  100 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7526 (t0)
REVERT: B  127 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7321 (mpp80)
REVERT: B  131 ASP cc_start: 0.6863 (p0) cc_final: 0.6615 (p0)
REVERT: B  146 SER cc_start: 0.8622 (t) cc_final: 0.8390 (t)
REVERT: B  155 ASN cc_start: 0.8277 (t0) cc_final: 0.7927 (t0)
REVERT: B  156 ASP cc_start: 0.7639 (p0) cc_final: 0.7333 (p0)
REVERT: B  231 ASP cc_start: 0.8012 (m-30) cc_final: 0.7796 (m-30)
REVERT: B  336 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7084 (tm-30)
REVERT: B  360 MET cc_start: 0.7820 (mmt) cc_final: 0.7385 (mmm)
REVERT: B  372 ARG cc_start: 0.7295 (mmt180) cc_final: 0.6597 (mmt180)
REVERT: C   21 MET cc_start: 0.8315 (mmm) cc_final: 0.7922 (mmm)
REVERT: C   91 MET cc_start: 0.5346 (tpt) cc_final: 0.5032 (tpt)
REVERT: C  295 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7746 (mt)
REVERT: C  329 MET cc_start: 0.6560 (tpp) cc_final: 0.6198 (mpp)
REVERT: D  206 TRP cc_start: 0.8597 (t-100) cc_final: 0.8362 (t-100)
  outliers start: 39
  outliers final: 18
  residues processed: 316
  average time/residue: 0.2964
  time to fit residues: 127.7013
Evaluate side-chains
  315 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 290
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  623 VAL
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  837 GLU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain D residue  272 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 67 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
A 480 GLN
A 557 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
A 771 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 358 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.171027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.141863 restraints weight = 16159.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.65
r_work: 0.3672 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10627  Z= 0.208
  Angle     :  0.620  13.572  14352  Z= 0.307
  Chirality :  0.042   0.206   1534
  Planarity :  0.004   0.048   1862
  Dihedral  :  4.185  21.816   1408
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 27.65 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.24), residues: 1260
  helix:  1.43 (0.20), residues: 666
  sheet: -0.38 (0.63), residues: 75
  loop : -0.86 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 560 
 HIS   0.004   0.001   HIS C 297 
 PHE   0.020   0.001   PHE C 275 
 TYR   0.026   0.002   TYR D 329 
 ARG   0.006   0.000   ARG A 315 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 292
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 GLU cc_start: 0.6840 (pm20) cc_final: 0.6594 (pm20)
REVERT: A  456 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6525 (mm-30)
REVERT: A  457 ASP cc_start: 0.7566 (m-30) cc_final: 0.7053 (m-30)
REVERT: A  458 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7184 (mt-10)
REVERT: A  470 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (mm)
REVERT: A  519 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7351 (mtmm)
REVERT: A  522 GLU cc_start: 0.7369 (mp0) cc_final: 0.7129 (mp0)
REVERT: A  559 ILE cc_start: 0.7525 (mt) cc_final: 0.7150 (mt)
REVERT: A  580 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7787 (mtmm)
REVERT: A  597 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7584 (mt-10)
REVERT: A  601 ASP cc_start: 0.7039 (m-30) cc_final: 0.6758 (m-30)
REVERT: A  625 GLU cc_start: 0.6775 (pm20) cc_final: 0.6073 (pm20)
REVERT: A  643 ARG cc_start: 0.6927 (mtt-85) cc_final: 0.6606 (mtt-85)
REVERT: A  741 SER cc_start: 0.8340 (t) cc_final: 0.7602 (p)
REVERT: A  746 ASN cc_start: 0.8295 (p0) cc_final: 0.8078 (p0)
REVERT: A  776 GLU cc_start: 0.7319 (tp30) cc_final: 0.6921 (tp30)
REVERT: A  787 LEU cc_start: 0.4425 (OUTLIER) cc_final: 0.4191 (tt)
REVERT: A  822 MET cc_start: 0.7805 (ttm) cc_final: 0.7452 (ttm)
REVERT: A  835 GLN cc_start: 0.7421 (mp10) cc_final: 0.7082 (mp10)
REVERT: A  854 MET cc_start: 0.8395 (mmm) cc_final: 0.8125 (mmt)
REVERT: A  855 ASP cc_start: 0.7364 (p0) cc_final: 0.6954 (p0)
REVERT: A  856 LYS cc_start: 0.7882 (mttm) cc_final: 0.7475 (mptt)
REVERT: A  915 MET cc_start: 0.6401 (mpp) cc_final: 0.5978 (mpp)
REVERT: A  922 LYS cc_start: 0.8265 (tmmt) cc_final: 0.7616 (tptm)
REVERT: A  925 PHE cc_start: 0.8007 (m-80) cc_final: 0.7460 (m-80)
REVERT: A  935 THR cc_start: 0.8310 (m) cc_final: 0.7726 (t)
REVERT: B   49 TYR cc_start: 0.6372 (p90) cc_final: 0.6129 (p90)
REVERT: B   74 ILE cc_start: 0.7524 (mm) cc_final: 0.7182 (mm)
REVERT: B   75 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7384 (mtmm)
REVERT: B   91 GLN cc_start: 0.8231 (mt0) cc_final: 0.7974 (mt0)
REVERT: B   92 MET cc_start: 0.8451 (ttt) cc_final: 0.8102 (ttm)
REVERT: B  100 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7421 (t0)
REVERT: B  127 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7253 (mpp80)
REVERT: B  131 ASP cc_start: 0.6826 (p0) cc_final: 0.6602 (p0)
REVERT: B  146 SER cc_start: 0.8617 (t) cc_final: 0.8384 (t)
REVERT: B  155 ASN cc_start: 0.8203 (t0) cc_final: 0.7877 (t0)
REVERT: B  156 ASP cc_start: 0.7632 (p0) cc_final: 0.7334 (p0)
REVERT: B  336 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7050 (tm-30)
REVERT: B  360 MET cc_start: 0.7883 (mmt) cc_final: 0.7374 (mmm)
REVERT: C   21 MET cc_start: 0.8296 (mmm) cc_final: 0.7484 (mmm)
REVERT: C   91 MET cc_start: 0.5422 (tpt) cc_final: 0.5088 (tpt)
REVERT: C  272 LYS cc_start: 0.7519 (ptpt) cc_final: 0.7318 (pttm)
REVERT: C  295 LEU cc_start: 0.8016 (mm) cc_final: 0.7742 (mt)
REVERT: C  329 MET cc_start: 0.6512 (tpp) cc_final: 0.6144 (mpp)
REVERT: D  206 TRP cc_start: 0.8582 (t-100) cc_final: 0.8349 (t-100)
  outliers start: 43
  outliers final: 20
  residues processed: 313
  average time/residue: 0.2838
  time to fit residues: 120.7545
Evaluate side-chains
  313 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 288
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 111 optimal weight:    0.0980
   chunk 8 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 480 GLN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
A 773 GLN
A 859 GLN
** B  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 261 GLN
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.170882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142179 restraints weight = 16293.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.60
r_work: 0.3679 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10627  Z= 0.213
  Angle     :  0.625  13.275  14352  Z= 0.309
  Chirality :  0.042   0.225   1534
  Planarity :  0.004   0.047   1862
  Dihedral  :  4.179  21.990   1408
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 28.18 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.24), residues: 1260
  helix:  1.48 (0.20), residues: 666
  sheet: -0.27 (0.63), residues: 75
  loop : -0.83 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 428 
 HIS   0.003   0.001   HIS A 453 
 PHE   0.028   0.002   PHE B 188 
 TYR   0.029   0.002   TYR B  16 
 ARG   0.006   0.000   ARG A 762 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 301
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 TYR cc_start: 0.7520 (m-10) cc_final: 0.7093 (m-10)
REVERT: A  456 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6738 (mm-30)
REVERT: A  457 ASP cc_start: 0.7547 (m-30) cc_final: 0.7050 (m-30)
REVERT: A  458 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7159 (mt-10)
REVERT: A  470 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8267 (mm)
REVERT: A  519 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7523 (mtmm)
REVERT: A  522 GLU cc_start: 0.7385 (mp0) cc_final: 0.7123 (mp0)
REVERT: A  582 ASN cc_start: 0.7542 (m-40) cc_final: 0.7339 (m-40)
REVERT: A  597 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7567 (mt-10)
REVERT: A  601 ASP cc_start: 0.7071 (m-30) cc_final: 0.6784 (m-30)
REVERT: A  625 GLU cc_start: 0.6921 (pm20) cc_final: 0.6220 (pm20)
REVERT: A  741 SER cc_start: 0.8263 (t) cc_final: 0.7582 (p)
REVERT: A  743 PHE cc_start: 0.8194 (t80) cc_final: 0.7991 (t80)
REVERT: A  746 ASN cc_start: 0.8268 (p0) cc_final: 0.8057 (p0)
REVERT: A  776 GLU cc_start: 0.7321 (tp30) cc_final: 0.6932 (tp30)
REVERT: A  787 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4226 (tt)
REVERT: A  822 MET cc_start: 0.7734 (ttm) cc_final: 0.7424 (ttm)
REVERT: A  835 GLN cc_start: 0.7375 (mp10) cc_final: 0.7036 (mp10)
REVERT: A  854 MET cc_start: 0.8386 (mmm) cc_final: 0.8153 (mmt)
REVERT: A  855 ASP cc_start: 0.7406 (p0) cc_final: 0.7080 (p0)
REVERT: A  856 LYS cc_start: 0.7928 (mttm) cc_final: 0.7561 (mptt)
REVERT: A  915 MET cc_start: 0.6481 (mpp) cc_final: 0.6131 (mpp)
REVERT: A  922 LYS cc_start: 0.8211 (tmmt) cc_final: 0.7590 (tptm)
REVERT: A  925 PHE cc_start: 0.8125 (m-80) cc_final: 0.7636 (m-80)
REVERT: A  935 THR cc_start: 0.8292 (m) cc_final: 0.7570 (p)
REVERT: B   74 ILE cc_start: 0.7549 (mm) cc_final: 0.7221 (mm)
REVERT: B   75 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7422 (mttp)
REVERT: B   91 GLN cc_start: 0.8211 (mt0) cc_final: 0.8001 (mt0)
REVERT: B   92 MET cc_start: 0.8521 (ttt) cc_final: 0.8193 (ttm)
REVERT: B  124 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6981 (mtpt)
REVERT: B  127 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7204 (mpp80)
REVERT: B  129 GLN cc_start: 0.7579 (mt0) cc_final: 0.7366 (mt0)
REVERT: B  131 ASP cc_start: 0.6773 (p0) cc_final: 0.6541 (p0)
REVERT: B  146 SER cc_start: 0.8686 (t) cc_final: 0.8442 (t)
REVERT: B  155 ASN cc_start: 0.8249 (t0) cc_final: 0.7903 (t0)
REVERT: B  156 ASP cc_start: 0.7628 (p0) cc_final: 0.7357 (p0)
REVERT: B  336 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6949 (mm-30)
REVERT: B  360 MET cc_start: 0.7771 (mmt) cc_final: 0.7369 (mmm)
REVERT: C   21 MET cc_start: 0.8288 (mmm) cc_final: 0.7543 (mmm)
REVERT: C   91 MET cc_start: 0.5378 (tpt) cc_final: 0.5028 (tpt)
REVERT: C  295 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7760 (mt)
REVERT: C  329 MET cc_start: 0.6538 (tpp) cc_final: 0.6180 (mpp)
REVERT: D  206 TRP cc_start: 0.8579 (t-100) cc_final: 0.8343 (t-100)
  outliers start: 40
  outliers final: 26
  residues processed: 323
  average time/residue: 0.2685
  time to fit residues: 116.5995
Evaluate side-chains
  325 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 294
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  837 GLU
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  284 ILE
Chi-restraints excluded: chain D residue  295 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 101 optimal weight:    0.5980
   chunk 125 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 49 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0010
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 ASN
B  45 ASN
B 112 GLN
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 308 ASN
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.170609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142009 restraints weight = 16400.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 2.59
r_work: 0.3674 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10627  Z= 0.212
  Angle     :  0.632  13.035  14352  Z= 0.315
  Chirality :  0.043   0.390   1534
  Planarity :  0.004   0.065   1862
  Dihedral  :  4.169  22.640   1408
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 28.53 %
    Favored  : 68.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.24), residues: 1260
  helix:  1.41 (0.20), residues: 673
  sheet: -0.33 (0.62), residues: 75
  loop : -0.82 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 313 
 HIS   0.003   0.001   HIS C 297 
 PHE   0.026   0.001   PHE B 188 
 TYR   0.034   0.001   TYR B  16 
 ARG   0.006   0.000   ARG A 762 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 298
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 TYR cc_start: 0.7385 (m-10) cc_final: 0.7117 (m-10)
REVERT: A  456 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6725 (mm-30)
REVERT: A  457 ASP cc_start: 0.7551 (m-30) cc_final: 0.7038 (m-30)
REVERT: A  458 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7046 (mt-10)
REVERT: A  470 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8247 (mm)
REVERT: A  492 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5140 (pm20)
REVERT: A  519 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7557 (mtmm)
REVERT: A  597 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: A  601 ASP cc_start: 0.7105 (m-30) cc_final: 0.6826 (m-30)
REVERT: A  625 GLU cc_start: 0.6925 (pm20) cc_final: 0.6242 (pm20)
REVERT: A  643 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6485 (mtt-85)
REVERT: A  741 SER cc_start: 0.8229 (t) cc_final: 0.7594 (p)
REVERT: A  752 PHE cc_start: 0.7967 (t80) cc_final: 0.7514 (t80)
REVERT: A  776 GLU cc_start: 0.7291 (tp30) cc_final: 0.6904 (tp30)
REVERT: A  787 LEU cc_start: 0.4363 (OUTLIER) cc_final: 0.4163 (tt)
REVERT: A  822 MET cc_start: 0.7716 (ttm) cc_final: 0.7397 (ttm)
REVERT: A  835 GLN cc_start: 0.7355 (mp10) cc_final: 0.7137 (mp10)
REVERT: A  854 MET cc_start: 0.8421 (mmm) cc_final: 0.8164 (mmt)
REVERT: A  855 ASP cc_start: 0.7495 (p0) cc_final: 0.7140 (p0)
REVERT: A  856 LYS cc_start: 0.7967 (mttm) cc_final: 0.7604 (mptt)
REVERT: A  863 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.7080 (ttm-80)
REVERT: A  915 MET cc_start: 0.6527 (mpp) cc_final: 0.6288 (mpp)
REVERT: A  922 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7230 (tptm)
REVERT: A  925 PHE cc_start: 0.8180 (m-80) cc_final: 0.7689 (m-80)
REVERT: A  935 THR cc_start: 0.8367 (m) cc_final: 0.7728 (p)
REVERT: A  937 GLU cc_start: 0.7957 (pt0) cc_final: 0.7720 (pm20)
REVERT: B   74 ILE cc_start: 0.7567 (mm) cc_final: 0.7233 (mm)
REVERT: B   91 GLN cc_start: 0.8224 (mt0) cc_final: 0.8018 (mt0)
REVERT: B   92 MET cc_start: 0.8550 (ttt) cc_final: 0.8189 (ttm)
REVERT: B  100 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7433 (t0)
REVERT: B  127 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7271 (mpp80)
REVERT: B  131 ASP cc_start: 0.6752 (p0) cc_final: 0.6545 (p0)
REVERT: B  146 SER cc_start: 0.8716 (t) cc_final: 0.8498 (t)
REVERT: B  155 ASN cc_start: 0.8240 (t0) cc_final: 0.7891 (t0)
REVERT: B  156 ASP cc_start: 0.7642 (p0) cc_final: 0.7435 (p0)
REVERT: B  185 GLU cc_start: 0.7631 (tt0) cc_final: 0.7312 (tt0)
REVERT: B  222 TYR cc_start: 0.8134 (m-10) cc_final: 0.7824 (m-10)
REVERT: B  336 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6944 (mm-30)
REVERT: B  360 MET cc_start: 0.7790 (mmt) cc_final: 0.7393 (mmm)
REVERT: C   20 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7353 (tt)
REVERT: C   21 MET cc_start: 0.8284 (mmm) cc_final: 0.7561 (mmm)
REVERT: C   91 MET cc_start: 0.5410 (tpt) cc_final: 0.5028 (tpt)
REVERT: C  295 LEU cc_start: 0.8043 (mm) cc_final: 0.7743 (mt)
REVERT: C  329 MET cc_start: 0.6575 (tpp) cc_final: 0.6187 (mpp)
REVERT: D  206 TRP cc_start: 0.8580 (t-100) cc_final: 0.8341 (t-100)
  outliers start: 37
  outliers final: 22
  residues processed: 317
  average time/residue: 0.2779
  time to fit residues: 119.1082
Evaluate side-chains
  323 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 294
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  837 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain C residue  308 MET
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 112 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0060
   chunk 51 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 480 GLN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 GLN
B 240 GLN    A
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 308 ASN
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.170259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.141304 restraints weight = 16094.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.59
r_work: 0.3670 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10627  Z= 0.209
  Angle     :  0.656  13.158  14352  Z= 0.325
  Chirality :  0.044   0.423   1534
  Planarity :  0.004   0.063   1862
  Dihedral  :  4.203  24.659   1408
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 28.18 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.24), residues: 1260
  helix:  1.35 (0.20), residues: 689
  sheet: -0.25 (0.62), residues: 75
  loop : -0.79 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 313 
 HIS   0.003   0.001   HIS C 297 
 PHE   0.034   0.002   PHE A 743 
 TYR   0.038   0.002   TYR B  16 
 ARG   0.013   0.001   ARG A 315 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 298
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 TYR cc_start: 0.7407 (m-10) cc_final: 0.7068 (m-10)
REVERT: A  456 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6347 (mm-30)
REVERT: A  457 ASP cc_start: 0.7571 (m-30) cc_final: 0.7045 (m-30)
REVERT: A  458 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7192 (mt-10)
REVERT: A  470 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8240 (mm)
REVERT: A  492 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5182 (pm20)
REVERT: A  519 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7353 (mtmm)
REVERT: A  522 GLU cc_start: 0.7347 (mp0) cc_final: 0.6850 (mp0)
REVERT: A  597 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: A  601 ASP cc_start: 0.7219 (m-30) cc_final: 0.6936 (m-30)
REVERT: A  625 GLU cc_start: 0.6979 (pm20) cc_final: 0.6326 (pm20)
REVERT: A  643 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6452 (mtt-85)
REVERT: A  741 SER cc_start: 0.8201 (t) cc_final: 0.7558 (p)
REVERT: A  752 PHE cc_start: 0.8132 (t80) cc_final: 0.7668 (t80)
REVERT: A  776 GLU cc_start: 0.7375 (tp30) cc_final: 0.7018 (tp30)
REVERT: A  787 LEU cc_start: 0.4394 (OUTLIER) cc_final: 0.4191 (tt)
REVERT: A  822 MET cc_start: 0.7656 (ttm) cc_final: 0.7422 (ttm)
REVERT: A  854 MET cc_start: 0.8503 (mmm) cc_final: 0.8277 (mmt)
REVERT: A  855 ASP cc_start: 0.7514 (p0) cc_final: 0.7166 (p0)
REVERT: A  856 LYS cc_start: 0.7957 (mttm) cc_final: 0.7600 (mptt)
REVERT: A  863 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.7067 (ttm-80)
REVERT: A  922 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7124 (tptm)
REVERT: A  925 PHE cc_start: 0.8224 (m-80) cc_final: 0.7756 (m-80)
REVERT: A  935 THR cc_start: 0.8356 (m) cc_final: 0.7766 (p)
REVERT: A  937 GLU cc_start: 0.7956 (pt0) cc_final: 0.7728 (pm20)
REVERT: B   91 GLN cc_start: 0.8200 (mt0) cc_final: 0.7964 (mt0)
REVERT: B   92 MET cc_start: 0.8559 (ttt) cc_final: 0.8199 (ttm)
REVERT: B  100 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7562 (t70)
REVERT: B  127 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7315 (mpp80)
REVERT: B  146 SER cc_start: 0.8749 (t) cc_final: 0.8521 (t)
REVERT: B  155 ASN cc_start: 0.8259 (t0) cc_final: 0.7991 (t0)
REVERT: B  156 ASP cc_start: 0.7680 (p0) cc_final: 0.7412 (p0)
REVERT: B  185 GLU cc_start: 0.7559 (tt0) cc_final: 0.7146 (tt0)
REVERT: B  188 PHE cc_start: 0.7871 (m-80) cc_final: 0.7551 (m-10)
REVERT: B  307 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7029 (ptt-90)
REVERT: B  336 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6965 (mm-30)
REVERT: B  360 MET cc_start: 0.7834 (mmt) cc_final: 0.7319 (mmm)
REVERT: C   21 MET cc_start: 0.8286 (mmm) cc_final: 0.7562 (mmm)
REVERT: C   91 MET cc_start: 0.5502 (tpt) cc_final: 0.5136 (tpt)
REVERT: C  295 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (mt)
REVERT: C  329 MET cc_start: 0.6647 (tpp) cc_final: 0.6247 (mpp)
REVERT: D  206 TRP cc_start: 0.8586 (t-100) cc_final: 0.8344 (t-100)
  outliers start: 40
  outliers final: 26
  residues processed: 319
  average time/residue: 0.2702
  time to fit residues: 115.6224
Evaluate side-chains
  334 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 300
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  837 GLU
Chi-restraints excluded: chain A residue  871 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  307 ARG
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain C residue  308 MET
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 102 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 8 optimal weight:   30.0000
   chunk 38 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 GLN
B 308 ASN
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.169034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.140585 restraints weight = 16140.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 2.55
r_work: 0.3666 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10627  Z= 0.231
  Angle     :  0.692  12.959  14352  Z= 0.341
  Chirality :  0.044   0.374   1534
  Planarity :  0.005   0.106   1862
  Dihedral  :  4.238  23.535   1408
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 28.71 %
    Favored  : 68.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1260
  helix:  1.23 (0.20), residues: 691
  sheet: -0.06 (0.63), residues: 74
  loop : -0.80 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 428 
 HIS   0.003   0.001   HIS C  79 
 PHE   0.026   0.002   PHE A 743 
 TYR   0.039   0.002   TYR B  16 
 ARG   0.009   0.001   ARG A 315 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 300
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 PHE cc_start: 0.7605 (t80) cc_final: 0.7113 (t80)
REVERT: A  401 TYR cc_start: 0.7407 (m-10) cc_final: 0.7078 (m-10)
REVERT: A  456 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6539 (mm-30)
REVERT: A  457 ASP cc_start: 0.7576 (m-30) cc_final: 0.7030 (m-30)
REVERT: A  458 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7200 (mt-10)
REVERT: A  470 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8246 (mm)
REVERT: A  492 GLU cc_start: 0.5764 (OUTLIER) cc_final: 0.5274 (pm20)
REVERT: A  519 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7453 (mtmm)
REVERT: A  522 GLU cc_start: 0.7389 (mp0) cc_final: 0.6901 (mp0)
REVERT: A  548 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: A  597 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7615 (mt-10)
REVERT: A  601 ASP cc_start: 0.7282 (m-30) cc_final: 0.6994 (m-30)
REVERT: A  625 GLU cc_start: 0.7025 (pm20) cc_final: 0.5964 (mp0)
REVERT: A  643 ARG cc_start: 0.7372 (mtt90) cc_final: 0.6511 (mtt-85)
REVERT: A  667 PHE cc_start: 0.5990 (m-80) cc_final: 0.5712 (m-80)
REVERT: A  752 PHE cc_start: 0.8170 (t80) cc_final: 0.7699 (t80)
REVERT: A  776 GLU cc_start: 0.7413 (tp30) cc_final: 0.6944 (tp30)
REVERT: A  822 MET cc_start: 0.7657 (ttm) cc_final: 0.7264 (ttm)
REVERT: A  854 MET cc_start: 0.8535 (mmm) cc_final: 0.8274 (mmt)
REVERT: A  855 ASP cc_start: 0.7546 (p0) cc_final: 0.7190 (p0)
REVERT: A  856 LYS cc_start: 0.8004 (mttm) cc_final: 0.7631 (mptt)
REVERT: A  863 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.7107 (ttm-80)
REVERT: A  922 LYS cc_start: 0.8173 (tmmt) cc_final: 0.7213 (tptm)
REVERT: A  925 PHE cc_start: 0.8272 (m-80) cc_final: 0.8062 (m-80)
REVERT: A  935 THR cc_start: 0.8400 (m) cc_final: 0.7878 (p)
REVERT: A  937 GLU cc_start: 0.7999 (pt0) cc_final: 0.7711 (pm20)
REVERT: B   74 ILE cc_start: 0.7633 (mm) cc_final: 0.7310 (mm)
REVERT: B   91 GLN cc_start: 0.8175 (mt0) cc_final: 0.7946 (mt0)
REVERT: B   92 MET cc_start: 0.8564 (ttt) cc_final: 0.8224 (ttm)
REVERT: B  100 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7546 (t70)
REVERT: B  127 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7265 (mpp80)
REVERT: B  129 GLN cc_start: 0.7628 (mt0) cc_final: 0.7381 (mt0)
REVERT: B  146 SER cc_start: 0.8769 (t) cc_final: 0.8549 (t)
REVERT: B  155 ASN cc_start: 0.8238 (t0) cc_final: 0.7967 (t0)
REVERT: B  156 ASP cc_start: 0.7746 (p0) cc_final: 0.7470 (p0)
REVERT: B  185 GLU cc_start: 0.7740 (tt0) cc_final: 0.7289 (tt0)
REVERT: B  188 PHE cc_start: 0.7833 (m-80) cc_final: 0.7519 (m-10)
REVERT: B  231 ASP cc_start: 0.7988 (m-30) cc_final: 0.7626 (m-30)
REVERT: B  294 LEU cc_start: 0.8592 (mp) cc_final: 0.8335 (mt)
REVERT: B  307 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7110 (ptt-90)
REVERT: B  336 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6932 (mm-30)
REVERT: B  360 MET cc_start: 0.7853 (mmt) cc_final: 0.7320 (mmm)
REVERT: C   21 MET cc_start: 0.8298 (mmm) cc_final: 0.7587 (mmm)
REVERT: C   91 MET cc_start: 0.5425 (tpt) cc_final: 0.5034 (tpt)
REVERT: C  295 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7812 (mt)
REVERT: C  329 MET cc_start: 0.6637 (tpp) cc_final: 0.6171 (mpp)
REVERT: D  206 TRP cc_start: 0.8578 (t-100) cc_final: 0.8332 (t-100)
  outliers start: 37
  outliers final: 27
  residues processed: 320
  average time/residue: 0.2626
  time to fit residues: 113.4067
Evaluate side-chains
  330 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 296
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  834 THR
Chi-restraints excluded: chain A residue  837 GLU
Chi-restraints excluded: chain A residue  871 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  307 ARG
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain C residue  308 MET
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 109 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 GLN
B 308 ASN
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 265 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.166542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.138133 restraints weight = 15935.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.53
r_work: 0.3646 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10627  Z= 0.256
  Angle     :  0.713  12.850  14352  Z= 0.352
  Chirality :  0.045   0.392   1534
  Planarity :  0.005   0.110   1862
  Dihedral  :  4.336  25.485   1408
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 29.42 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.24), residues: 1260
  helix:  1.12 (0.20), residues: 692
  sheet: -0.21 (0.62), residues: 74
  loop : -0.84 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 428 
 HIS   0.004   0.001   HIS B  40 
 PHE   0.031   0.002   PHE A 362 
 TYR   0.035   0.002   TYR B  16 
 ARG   0.010   0.001   ARG A 315 

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 308
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 SER cc_start: 0.7354 (t) cc_final: 0.6992 (p)
REVERT: A  322 GLU cc_start: 0.6945 (pm20) cc_final: 0.6476 (pm20)
REVERT: A  365 PHE cc_start: 0.7629 (t80) cc_final: 0.7149 (t80)
REVERT: A  401 TYR cc_start: 0.7438 (m-10) cc_final: 0.7142 (m-10)
REVERT: A  448 TYR cc_start: 0.7351 (m-80) cc_final: 0.7115 (m-80)
REVERT: A  456 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6513 (mm-30)
REVERT: A  457 ASP cc_start: 0.7603 (m-30) cc_final: 0.7056 (m-30)
REVERT: A  458 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7228 (mt-10)
REVERT: A  463 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.6957 (t0)
REVERT: A  470 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8276 (mm)
REVERT: A  492 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5416 (pm20)
REVERT: A  519 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7526 (mtmm)
REVERT: A  522 GLU cc_start: 0.7433 (mp0) cc_final: 0.6873 (mp0)
REVERT: A  546 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: A  548 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7055 (tm-30)
REVERT: A  597 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7495 (mt-10)
REVERT: A  601 ASP cc_start: 0.7436 (m-30) cc_final: 0.7153 (m-30)
REVERT: A  625 GLU cc_start: 0.6885 (pm20) cc_final: 0.5911 (mt-10)
REVERT: A  643 ARG cc_start: 0.7478 (mtt90) cc_final: 0.6913 (mtt90)
REVERT: A  652 GLN cc_start: 0.6766 (mm110) cc_final: 0.6415 (mm110)
REVERT: A  746 ASN cc_start: 0.8177 (p0) cc_final: 0.7954 (p0)
REVERT: A  752 PHE cc_start: 0.8216 (t80) cc_final: 0.7738 (t80)
REVERT: A  822 MET cc_start: 0.7622 (ttm) cc_final: 0.7380 (ttm)
REVERT: A  854 MET cc_start: 0.8560 (mmm) cc_final: 0.8262 (mmt)
REVERT: A  855 ASP cc_start: 0.7688 (p0) cc_final: 0.7257 (p0)
REVERT: A  856 LYS cc_start: 0.8091 (mttm) cc_final: 0.7704 (mptt)
REVERT: A  863 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.7237 (ttm-80)
REVERT: A  915 MET cc_start: 0.6291 (mpp) cc_final: 0.5746 (ttt)
REVERT: A  922 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7558 (tptm)
REVERT: A  928 ARG cc_start: 0.6862 (ptm160) cc_final: 0.6575 (ptm160)
REVERT: A  935 THR cc_start: 0.8452 (m) cc_final: 0.7935 (p)
REVERT: A  937 GLU cc_start: 0.8018 (pt0) cc_final: 0.7599 (pt0)
REVERT: B   74 ILE cc_start: 0.7661 (mm) cc_final: 0.7344 (mm)
REVERT: B   91 GLN cc_start: 0.8226 (mt0) cc_final: 0.8014 (mt0)
REVERT: B   92 MET cc_start: 0.8519 (ttt) cc_final: 0.8191 (ttm)
REVERT: B  100 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7525 (t70)
REVERT: B  127 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7296 (mpp80)
REVERT: B  129 GLN cc_start: 0.7712 (mt0) cc_final: 0.7449 (mt0)
REVERT: B  155 ASN cc_start: 0.8298 (t0) cc_final: 0.8026 (t0)
REVERT: B  156 ASP cc_start: 0.7729 (p0) cc_final: 0.7434 (p0)
REVERT: B  185 GLU cc_start: 0.7645 (tt0) cc_final: 0.7221 (tt0)
REVERT: B  188 PHE cc_start: 0.7905 (m-80) cc_final: 0.7573 (m-10)
REVERT: B  202 TYR cc_start: 0.8098 (t80) cc_final: 0.7291 (t80)
REVERT: B  231 ASP cc_start: 0.8021 (m-30) cc_final: 0.7656 (m-30)
REVERT: B  307 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7152 (ptt-90)
REVERT: B  336 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7080 (mm-30)
REVERT: B  360 MET cc_start: 0.7838 (mmt) cc_final: 0.7393 (mmm)
REVERT: C   21 MET cc_start: 0.8309 (mmm) cc_final: 0.7591 (mmm)
REVERT: C   91 MET cc_start: 0.5477 (tpt) cc_final: 0.5047 (tpt)
REVERT: C  295 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7798 (mt)
REVERT: C  329 MET cc_start: 0.6735 (tpp) cc_final: 0.6246 (mpp)
REVERT: D  206 TRP cc_start: 0.8592 (t-100) cc_final: 0.8336 (t-100)
  outliers start: 34
  outliers final: 22
  residues processed: 324
  average time/residue: 0.2684
  time to fit residues: 118.5446
Evaluate side-chains
  335 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 305
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  519 LYS
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  607 HIS
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  837 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  307 ARG
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  282 ARG
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain C residue  308 MET
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0030
   chunk 57 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0470
   chunk 118 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0770
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   overall best weight:    0.2046

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 308 ASN
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 265 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.170853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.143050 restraints weight = 16172.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.56
r_work: 0.3685 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.4309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10627  Z= 0.193
  Angle     :  0.689  13.199  14352  Z= 0.342
  Chirality :  0.043   0.365   1534
  Planarity :  0.004   0.066   1862
  Dihedral  :  4.204  24.249   1408
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 30.21 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1260
  helix:  1.23 (0.20), residues: 695
  sheet: -0.22 (0.64), residues: 75
  loop : -0.83 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 428 
 HIS   0.004   0.001   HIS B  40 
 PHE   0.030   0.002   PHE A 743 
 TYR   0.024   0.002   TYR B  16 
 ARG   0.022   0.001   ARG A 315 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5338.46 seconds
wall clock time: 95 minutes 25.41 seconds (5725.41 seconds total)