Starting phenix.real_space_refine
on Wed Mar  4 09:25:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l49_23158/03_2026/7l49_23158.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l49_23158/03_2026/7l49_23158.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l49_23158/03_2026/7l49_23158.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l49_23158/03_2026/7l49_23158.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l49_23158/03_2026/7l49_23158.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l49_23158/03_2026/7l49_23158.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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
     Zn      4      6.06       5
     P     190      5.49       5
     S      37      5.16       5
     C    7186      2.51       5
     N    2218      2.21       5
     O    2779      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12414
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 522, 4229
          Classifications: {'peptide': 522}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 17, 'TRANS': 504}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 46
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 4181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 519, 4181
          Classifications: {'peptide': 519}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 17, 'TRANS': 501}
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "C"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 599
          Classifications: {'DNA': 30}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 29}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {' DC%5*END:plan': 1, ' DC%5*END:plan2': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "D"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 429
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "E"
      Number of atoms: 2877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 2877
          Classifications: {'RNA': 135}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 59}
          Link IDs: {'rna2p': 14, 'rna3p': 120}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 95
          Classifications: {'DNA': 5}
          Link IDs: {'rna3p': 4}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3858  SG  CYS A 478       7.021  61.788  44.308  1.00 37.58           S
  ATOM   4048  SG  CYS A 500      10.720  61.502  41.558  1.00 40.36           S
  ATOM    364  SG  CYS A  50      53.252  98.716  77.958  1.00 42.34           S
  ATOM    502  SG  CYS A  69      57.157  99.263  78.476  1.00 31.65           S
  ATOM    527  SG  CYS A  72      55.385  96.180  79.439  1.00 31.06           S
  ATOM   8043  SG  CYS B 478      59.449  58.052   9.211  1.00 58.65           S
  ATOM   8229  SG  CYS B 500      56.592  59.678  11.519  1.00 65.09           S

  Time building chain proxies: 2.63, per 1000 atoms: 0.21
  Number of scatterers: 12414
  At special positions: 0
  Unit cell: (102.9, 121.8, 123.9, 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      4     29.99
     S      37     16.00
     P     190     15.00
     O    2779      8.00
     N    2218      7.00
     C    7186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 438.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 500 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 478 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A  72 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A  69 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A  50 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A  53 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 500 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 478 "
      Number of angles added : 3


  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      46.0% alpha, 10.5% beta
      59 base pairs and 115 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 42
    Processing helix  chain 'A' and resid 52 through 58
      removed outlier: 4.153A  pdb=" N   VAL A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA A  57 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ALA A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 58'
    Processing helix  chain 'A' and resid 70 through 75
      removed outlier: 3.678A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 89
      removed outlier: 3.931A  pdb=" N   TYR A  82 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 126
    Processing helix  chain 'A' and resid 133 through 153
      removed outlier: 4.575A  pdb=" N   TYR A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   THR A 147 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 170
      removed outlier: 3.644A  pdb=" N   ASN A 169 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 177
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 299
      removed outlier: 3.901A  pdb=" N   GLU A 298 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS A 299 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 295 through 299'
    Processing helix  chain 'A' and resid 350 through 367
    Processing helix  chain 'A' and resid 377 through 382
    Processing helix  chain 'A' and resid 382 through 414
      removed outlier: 3.707A  pdb=" N   THR A 386 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 387 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 444 through 458
    Processing helix  chain 'A' and resid 486 through 493
    Processing helix  chain 'A' and resid 508 through 518
      removed outlier: 3.597A  pdb=" N   ALA A 513 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 41
      removed outlier: 3.557A  pdb=" N   GLU B  24 " --> pdb=" O   SER B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 3.968A  pdb=" N   VAL B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 76
      removed outlier: 3.747A  pdb=" N   ALA B  74 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 89
      removed outlier: 3.626A  pdb=" N   TYR B  82 " --> pdb=" O   ASP B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 126
    Processing helix  chain 'B' and resid 133 through 144
      removed outlier: 3.664A  pdb=" N   VAL B 137 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 153
      removed outlier: 3.958A  pdb=" N   PHE B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 170
      removed outlier: 3.569A  pdb=" N   SER B 164 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 177
      removed outlier: 4.198A  pdb=" N   ASN B 177 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 280
      removed outlier: 3.612A  pdb=" N   GLU B 272 " --> pdb=" O   ASP B 268 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLU B 274 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 366
    Processing helix  chain 'B' and resid 377 through 382
      removed outlier: 3.991A  pdb=" N   LYS B 381 " --> pdb=" O   GLY B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 414
    Processing helix  chain 'B' and resid 423 through 429
    Processing helix  chain 'B' and resid 444 through 459
      removed outlier: 3.866A  pdb=" N   TYR B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 493
      removed outlier: 3.581A  pdb=" N   LYS B 492 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.632A  pdb=" N   ALA B 513 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218
      removed outlier: 4.340A  pdb=" N   PHE A 214 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   SER A 251 " --> pdb=" O   TYR A  18 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG A  16 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   TRP A 302 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   TYR A 287 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345
      removed outlier: 3.532A  pdb=" N   VAL A 334 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 8.416A  pdb=" N   VAL A 416 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ILE A 321 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE A 325 " --> pdb=" O   GLN A 420 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLU A 422 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   VAL A 327 " --> pdb=" O   GLU A 422 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   GLY A 417 " --> pdb=" O   GLU A 462 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   ARG A 464 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL A 419 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   VAL A 466 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   MET A 421 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 499
      removed outlier: 3.713A  pdb=" N   GLU A 507 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209
      removed outlier: 7.396A  pdb=" N   SER B 251 " --> pdb=" O   PRO B  17 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   LEU B 253 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER B 255 " --> pdb=" O   ARG B  13 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   TRP B 302 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   TYR B 287 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 259
    Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345
      removed outlier: 6.532A  pdb=" N   GLY B 323 " --> pdb=" O   GLN B 420 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 499

    376 hydrogen bonds defined for protein.
    1092 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      149 hydrogen bonds
      294 hydrogen bond angles
      0 basepair planarities
      59 basepair parallelities
      115 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.40 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: 3322
        1.34 -     1.47: 4068
        1.47 -     1.59: 5248
        1.59 -     1.71: 365
        1.71 -     1.84: 51
  Bond restraints: 13054
  Sorted by residual:
  bond pdb=" N   LYS B 383 "
       pdb=" CA  LYS B 383 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 9.20e-03 1.18e+04 1.19e+01
  bond pdb=" N   ILE B 385 "
       pdb=" CA  ILE B 385 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.039 1.19e-02 7.06e+03 1.05e+01
  bond pdb=" N   CYS B  50 "
       pdb=" CA  CYS B  50 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.65e+00
  bond pdb=" N   LEU B 382 "
       pdb=" CA  LEU B 382 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.42e-02 4.96e+03 6.96e+00
  bond pdb=" N   ARG A 438 "
       pdb=" CA  ARG A 438 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.42e-02 4.96e+03 6.94e+00
  ... (remaining 13049 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 17953
        2.53 -     5.06: 447
        5.06 -     7.59: 44
        7.59 -    10.12: 9
       10.12 -    12.65: 2
  Bond angle restraints: 18455
  Sorted by residual:
  angle pdb=" N   PRO B 384 "
        pdb=" CA  PRO B 384 "
        pdb=" C   PRO B 384 "
      ideal   model   delta    sigma   weight residual
     113.40  121.56   -8.16 1.34e+00 5.57e-01 3.71e+01
  angle pdb=" C   GLU B  65 "
        pdb=" N   ARG B  66 "
        pdb=" CA  ARG B  66 "
      ideal   model   delta    sigma   weight residual
     121.54  132.95  -11.41 1.91e+00 2.74e-01 3.57e+01
  angle pdb=" C4'   G E 190 "
        pdb=" C3'   G E 190 "
        pdb=" O3'   G E 190 "
      ideal   model   delta    sigma   weight residual
     109.40  117.19   -7.79 1.50e+00 4.44e-01 2.70e+01
  angle pdb=" C   CYS A 297 "
        pdb=" N   GLU A 298 "
        pdb=" CA  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     121.54  130.99   -9.45 1.91e+00 2.74e-01 2.45e+01
  angle pdb=" CA  TRP B 223 "
        pdb=" CB  TRP B 223 "
        pdb=" CG  TRP B 223 "
      ideal   model   delta    sigma   weight residual
     113.60  122.51   -8.91 1.90e+00 2.77e-01 2.20e+01
  ... (remaining 18450 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.71: 7306
       35.71 -    71.42: 590
       71.42 -   107.13: 41
      107.13 -   142.84: 2
      142.84 -   178.54: 2
  Dihedral angle restraints: 7941
    sinusoidal: 4874
      harmonic: 3067
  Sorted by residual:
  dihedral pdb=" O4'   U E  92 "
           pdb=" C1'   U E  92 "
           pdb=" N1    U E  92 "
           pdb=" C2    U E  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.46  178.54     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C E  77 "
           pdb=" C1'   C E  77 "
           pdb=" N1    C E  77 "
           pdb=" C2    C E  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   56.83  175.17     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   U E 110 "
           pdb=" C1'   U E 110 "
           pdb=" N1    U E 110 "
           pdb=" C2    U E 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -61.24  -98.76     1      1.50e+01 4.44e-03 4.92e+01
  ... (remaining 7938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1904
       0.093 -    0.186: 193
       0.186 -    0.279: 16
       0.279 -    0.372: 5
       0.372 -    0.465: 1
  Chirality restraints: 2119
  Sorted by residual:
  chirality pdb=" CB  ILE B 131 "
            pdb=" CA  ILE B 131 "
            pdb=" CG1 ILE B 131 "
            pdb=" CG2 ILE B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.47 2.00e-01 2.50e+01 5.42e+00
  chirality pdb=" C3'   G E 190 "
            pdb=" C4'   G E 190 "
            pdb=" O3'   G E 190 "
            pdb=" C2'   G E 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.41   -0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CB  THR A 389 "
            pdb=" CA  THR A 389 "
            pdb=" OG1 THR A 389 "
            pdb=" CG2 THR A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.23    0.32 2.00e-01 2.50e+01 2.61e+00
  ... (remaining 2116 not shown)

  Planarity restraints: 1666
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA C  42 "   -0.031 2.00e-02 2.50e+03   2.42e-02 1.61e+01
        pdb=" N9   DA C  42 "    0.064 2.00e-02 2.50e+03
        pdb=" C8   DA C  42 "   -0.033 2.00e-02 2.50e+03
        pdb=" N7   DA C  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA C  42 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA C  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA C  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1   DA C  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2   DA C  42 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DA C  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA C  42 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U E 197 "    0.024 2.00e-02 2.50e+03   2.31e-02 1.20e+01
        pdb=" N1    U E 197 "   -0.055 2.00e-02 2.50e+03
        pdb=" C2    U E 197 "    0.031 2.00e-02 2.50e+03
        pdb=" O2    U E 197 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3    U E 197 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    U E 197 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U E 197 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    U E 197 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    U E 197 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E 123 "    0.026 2.00e-02 2.50e+03   2.19e-02 1.08e+01
        pdb=" N1    C E 123 "   -0.056 2.00e-02 2.50e+03
        pdb=" C2    C E 123 "    0.021 2.00e-02 2.50e+03
        pdb=" O2    C E 123 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    C E 123 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    C E 123 "    0.002 2.00e-02 2.50e+03
        pdb=" N4    C E 123 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C E 123 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    C E 123 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1663 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1453
        2.76 -     3.29: 10809
        3.29 -     3.83: 22411
        3.83 -     4.36: 27377
        4.36 -     4.90: 41752
  Nonbonded interactions: 103802
  Sorted by model distance:
  nonbonded pdb=" N3    C E  22 "
            pdb=" N1    G E  71 "
     model   vdw
     2.220 3.200
  nonbonded pdb=" OG1 THR A   9 "
            pdb=" O2'   A E 203 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" N4    C E  22 "
            pdb=" O6    G E  71 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O2    C E  87 "
            pdb=" O2'   A E 129 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   PHE B 341 "
            pdb=" OH  TYR B 511 "
     model   vdw
     2.296 3.040
  ... (remaining 103797 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ 
rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298  \ 
or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid  \ 
300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 493 through 602))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.430
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
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      :  0.006   0.370  13062  Z= 0.274
  Angle     :  0.954  12.650  18458  Z= 0.552
  Chirality :  0.059   0.465   2119
  Planarity :  0.007   0.065   1666
  Dihedral  : 21.426 178.545   5951
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.90 (0.21), residues: 1037
  helix: -2.17 (0.19), residues: 444
  sheet: -2.23 (0.37), residues: 167
  loop : -3.07 (0.23), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  16 
 TYR   0.021   0.002   TYR B 113 
 PHE   0.026   0.002   PHE B 220 
 TRP   0.039   0.003   TRP B 223 
 HIS   0.014   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (13054)
  covalent geometry    : angle       0.94800 (18455)
  hydrogen bonds       : bond        0.13537 (  525)
  hydrogen bonds       : angle       6.51030 ( 1386)
  metal coordination   : bond        0.13335 (    8)
  metal coordination   : angle       8.41972 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 TYR cc_start: 0.6934 (m-80) cc_final: 0.6706 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1666
  time to fit residues: 28.0396
Evaluate side-chains
  87 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0770
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.1944

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 209 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 169 ASN
B 211 ASN
** B 480 HIS ** 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 = 0.4102 r_free = 0.4102 target = 0.182903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.139050 restraints weight = 13633.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.49
r_work: 0.3299 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.142  13062  Z= 0.201
  Angle     :  0.610  10.447  18458  Z= 0.325
  Chirality :  0.039   0.201   2119
  Planarity :  0.005   0.050   1666
  Dihedral  : 21.965 174.896   3799
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.13 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.24), residues: 1037
  helix: -0.39 (0.23), residues: 459
  sheet: -1.41 (0.41), residues: 155
  loop : -2.75 (0.25), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 373 
 TYR   0.016   0.002   TYR B 113 
 PHE   0.019   0.002   PHE B 454 
 TRP   0.012   0.002   TRP B 302 
 HIS   0.010   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (13054)
  covalent geometry    : angle       0.60352 (18455)
  hydrogen bonds       : bond        0.04708 (  525)
  hydrogen bonds       : angle       4.30885 ( 1386)
  metal coordination   : bond        0.05053 (    8)
  metal coordination   : angle       6.85852 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.329 
Fit side-chains
REVERT: B  276 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7974 (mmmm)
REVERT: B  343 ARG cc_start: 0.8211 (ptp-170) cc_final: 0.7745 (ptp-170)
  outliers start: 4
  outliers final: 3
  residues processed: 113
  average time/residue: 0.1570
  time to fit residues: 23.5678
Evaluate side-chains
  101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue  229 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 111 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 280 ASN
A 449 GLN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** 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 = 0.4036 r_free = 0.4036 target = 0.176260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.131211 restraints weight = 13814.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.54
r_work: 0.3203 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096  13062  Z= 0.274
  Angle     :  0.653  12.356  18458  Z= 0.346
  Chirality :  0.042   0.198   2119
  Planarity :  0.004   0.057   1666
  Dihedral  : 22.143 175.191   3799
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.25 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.25), residues: 1037
  helix:  0.13 (0.24), residues: 462
  sheet: -1.24 (0.43), residues: 151
  loop : -2.72 (0.25), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  16 
 TYR   0.020   0.002   TYR A  82 
 PHE   0.024   0.002   PHE B 205 
 TRP   0.012   0.002   TRP B 265 
 HIS   0.008   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 (13054)
  covalent geometry    : angle       0.64668 (18455)
  hydrogen bonds       : bond        0.05165 (  525)
  hydrogen bonds       : angle       4.18250 ( 1386)
  metal coordination   : bond        0.03415 (    8)
  metal coordination   : angle       7.29105 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.8618 (tptp) cc_final: 0.8404 (tptp)
REVERT: A  425 GLU cc_start: 0.7394 (tp30) cc_final: 0.6309 (pp20)
REVERT: B   98 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8120 (tt)
REVERT: B  138 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7980 (tp30)
REVERT: B  153 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8285 (p90)
REVERT: B  222 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7406 (mtp85)
REVERT: B  343 ARG cc_start: 0.8199 (ptp-170) cc_final: 0.7960 (ptp-170)
REVERT: B  362 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7935 (ttp-110)
REVERT: B  383 LYS cc_start: 0.7013 (tptp) cc_final: 0.6266 (mmtt)
  outliers start: 21
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1464
  time to fit residues: 23.5147
Evaluate side-chains
  105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 SER
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  282 ASP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  497 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 89 optimal weight:    0.2980
   chunk 114 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 87 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 155 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 516 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.182773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138284 restraints weight = 13767.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.50
r_work: 0.3308 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13062  Z= 0.136
  Angle     :  0.522   7.542  18458  Z= 0.279
  Chirality :  0.036   0.165   2119
  Planarity :  0.004   0.045   1666
  Dihedral  : 21.897 179.550   3799
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.59 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.26), residues: 1037
  helix:  0.75 (0.24), residues: 460
  sheet: -0.84 (0.45), residues: 142
  loop : -2.54 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  13 
 TYR   0.015   0.001   TYR B 113 
 PHE   0.014   0.001   PHE A 205 
 TRP   0.007   0.001   TRP B 265 
 HIS   0.004   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13054)
  covalent geometry    : angle       0.51993 (18455)
  hydrogen bonds       : bond        0.04206 (  525)
  hydrogen bonds       : angle       3.81450 ( 1386)
  metal coordination   : bond        0.01633 (    8)
  metal coordination   : angle       3.42514 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.8749 (tptp) cc_final: 0.8509 (tptp)
REVERT: A  341 PHE cc_start: 0.7245 (m-80) cc_final: 0.7033 (m-10)
REVERT: A  358 MET cc_start: 0.8431 (mmm) cc_final: 0.8152 (mmm)
REVERT: A  425 GLU cc_start: 0.7311 (tp30) cc_final: 0.6206 (pt0)
REVERT: A  438 ARG cc_start: 0.7869 (tpp-160) cc_final: 0.7544 (ttm110)
REVERT: B   98 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8009 (tt)
REVERT: B  138 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8017 (tp30)
REVERT: B  153 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7494 (p90)
REVERT: B  362 ARG cc_start: 0.8351 (mtp85) cc_final: 0.8002 (ttp-110)
REVERT: B  383 LYS cc_start: 0.7198 (tptp) cc_final: 0.6323 (mmtt)
  outliers start: 13
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1504
  time to fit residues: 24.0243
Evaluate side-chains
  100 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 114 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.181359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.137312 restraints weight = 13626.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.45
r_work: 0.3315 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13062  Z= 0.132
  Angle     :  0.503   7.536  18458  Z= 0.270
  Chirality :  0.036   0.153   2119
  Planarity :  0.003   0.038   1666
  Dihedral  : 21.836 179.567   3799
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.37 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1037
  helix:  1.06 (0.25), residues: 461
  sheet: -0.82 (0.44), residues: 150
  loop : -2.48 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  13 
 TYR   0.016   0.001   TYR B 113 
 PHE   0.014   0.001   PHE A 205 
 TRP   0.007   0.001   TRP B 443 
 HIS   0.003   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (13054)
  covalent geometry    : angle       0.50194 (18455)
  hydrogen bonds       : bond        0.04129 (  525)
  hydrogen bonds       : angle       3.69072 ( 1386)
  metal coordination   : bond        0.01338 (    8)
  metal coordination   : angle       3.10828 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8783 (tptp) cc_final: 0.8459 (tptp)
REVERT: A  341 PHE cc_start: 0.7215 (m-80) cc_final: 0.6951 (m-10)
REVERT: A  425 GLU cc_start: 0.7352 (tp30) cc_final: 0.6251 (pt0)
REVERT: A  438 ARG cc_start: 0.7853 (tpp-160) cc_final: 0.7535 (ttm110)
REVERT: B   98 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8111 (tt)
REVERT: B  138 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8030 (tp30)
REVERT: B  153 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7480 (p90)
REVERT: B  362 ARG cc_start: 0.8289 (mtp85) cc_final: 0.8075 (ttp-110)
REVERT: B  383 LYS cc_start: 0.7225 (tptp) cc_final: 0.6275 (mmtt)
REVERT: B  454 PHE cc_start: 0.8881 (t80) cc_final: 0.8657 (t80)
REVERT: B  481 LEU cc_start: 0.8090 (tp) cc_final: 0.7113 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1547
  time to fit residues: 22.8567
Evaluate side-chains
  103 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  517 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0270
   chunk 83 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 88 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.9242

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.181188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136717 restraints weight = 13611.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 1.55
r_work: 0.3270 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13062  Z= 0.161
  Angle     :  0.522   7.678  18458  Z= 0.279
  Chirality :  0.037   0.155   2119
  Planarity :  0.003   0.040   1666
  Dihedral  : 21.850 179.749   3799
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.48 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.26), residues: 1037
  helix:  1.15 (0.25), residues: 462
  sheet: -0.80 (0.44), residues: 151
  loop : -2.43 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  13 
 TYR   0.017   0.001   TYR A  82 
 PHE   0.013   0.001   PHE A 214 
 TRP   0.007   0.001   TRP A 265 
 HIS   0.004   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (13054)
  covalent geometry    : angle       0.52068 (18455)
  hydrogen bonds       : bond        0.04245 (  525)
  hydrogen bonds       : angle       3.71231 ( 1386)
  metal coordination   : bond        0.01384 (    8)
  metal coordination   : angle       3.37124 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8638 (tptp) cc_final: 0.8398 (tptp)
REVERT: A  231 LYS cc_start: 0.8426 (ptmm) cc_final: 0.8208 (pttp)
REVERT: A  425 GLU cc_start: 0.7285 (tp30) cc_final: 0.6347 (pt0)
REVERT: A  438 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7453 (ttm110)
REVERT: B   98 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8046 (tt)
REVERT: B  138 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7915 (tp30)
REVERT: B  153 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7647 (p90)
REVERT: B  383 LYS cc_start: 0.7303 (tptp) cc_final: 0.6282 (mmtt)
REVERT: B  481 LEU cc_start: 0.8000 (tp) cc_final: 0.7016 (mt)
  outliers start: 19
  outliers final: 10
  residues processed: 109
  average time/residue: 0.1503
  time to fit residues: 22.3389
Evaluate side-chains
  101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 56 optimal weight:   30.0000
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 GLN
** B 480 HIS ** 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 = 0.4091 r_free = 0.4091 target = 0.181827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137317 restraints weight = 13633.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.43
r_work: 0.3296 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13062  Z= 0.150
  Angle     :  0.518   9.048  18458  Z= 0.275
  Chirality :  0.037   0.216   2119
  Planarity :  0.003   0.038   1666
  Dihedral  : 21.819 179.766   3799
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.48 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1037
  helix:  1.18 (0.25), residues: 464
  sheet: -0.75 (0.44), residues: 151
  loop : -2.39 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  13 
 TYR   0.016   0.001   TYR B 113 
 PHE   0.016   0.001   PHE B 454 
 TRP   0.007   0.001   TRP A 265 
 HIS   0.003   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (13054)
  covalent geometry    : angle       0.51670 (18455)
  hydrogen bonds       : bond        0.04179 (  525)
  hydrogen bonds       : angle       3.68275 ( 1386)
  metal coordination   : bond        0.01120 (    8)
  metal coordination   : angle       2.86351 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8756 (tptp) cc_final: 0.8501 (tptp)
REVERT: A  425 GLU cc_start: 0.7336 (tp30) cc_final: 0.6238 (pt0)
REVERT: A  438 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7520 (ttm110)
REVERT: B   98 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8160 (tt)
REVERT: B  138 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7977 (tp30)
REVERT: B  153 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7716 (p90)
REVERT: B  383 LYS cc_start: 0.7380 (tptp) cc_final: 0.6315 (mmtt)
REVERT: B  454 PHE cc_start: 0.8918 (t80) cc_final: 0.8714 (t80)
REVERT: B  481 LEU cc_start: 0.8093 (tp) cc_final: 0.7123 (mt)
  outliers start: 19
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1500
  time to fit residues: 22.3328
Evaluate side-chains
  102 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 GLN
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 108 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.178736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.134929 restraints weight = 13683.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.52
r_work: 0.3228 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13062  Z= 0.209
  Angle     :  0.571   7.856  18458  Z= 0.303
  Chirality :  0.039   0.210   2119
  Planarity :  0.004   0.041   1666
  Dihedral  : 21.914 178.383   3799
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.70 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.26), residues: 1037
  helix:  1.10 (0.25), residues: 463
  sheet: -1.11 (0.43), residues: 159
  loop : -2.33 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  13 
 TYR   0.019   0.001   TYR A  82 
 PHE   0.017   0.002   PHE A 214 
 TRP   0.010   0.002   TRP A 265 
 HIS   0.005   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (13054)
  covalent geometry    : angle       0.56914 (18455)
  hydrogen bonds       : bond        0.04504 (  525)
  hydrogen bonds       : angle       3.79709 ( 1386)
  metal coordination   : bond        0.01477 (    8)
  metal coordination   : angle       3.82559 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8614 (tptp) cc_final: 0.8342 (tptp)
REVERT: A  425 GLU cc_start: 0.7364 (tp30) cc_final: 0.6395 (pt0)
REVERT: A  427 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6420 (mmt)
REVERT: B   98 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8147 (tt)
REVERT: B  138 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7944 (tp30)
REVERT: B  153 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7862 (p90)
REVERT: B  481 LEU cc_start: 0.8065 (tp) cc_final: 0.7063 (mt)
  outliers start: 20
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1465
  time to fit residues: 21.9421
Evaluate side-chains
  105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 56 optimal weight:   30.0000
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.182007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137451 restraints weight = 13647.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.50
r_work: 0.3289 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13062  Z= 0.139
  Angle     :  0.521   7.647  18458  Z= 0.278
  Chirality :  0.037   0.217   2119
  Planarity :  0.003   0.036   1666
  Dihedral  : 21.816 179.730   3799
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.71 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.26), residues: 1037
  helix:  1.22 (0.25), residues: 464
  sheet: -0.82 (0.45), residues: 147
  loop : -2.27 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 171 
 TYR   0.016   0.001   TYR B 113 
 PHE   0.013   0.001   PHE A 205 
 TRP   0.007   0.001   TRP B 443 
 HIS   0.003   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13054)
  covalent geometry    : angle       0.51978 (18455)
  hydrogen bonds       : bond        0.04141 (  525)
  hydrogen bonds       : angle       3.68503 ( 1386)
  metal coordination   : bond        0.00808 (    8)
  metal coordination   : angle       2.41946 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8592 (tptp) cc_final: 0.8339 (tptp)
REVERT: A  425 GLU cc_start: 0.7243 (tp30) cc_final: 0.6316 (pt0)
REVERT: B   98 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8027 (tt)
REVERT: B  138 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7894 (tp30)
REVERT: B  153 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7633 (p90)
REVERT: B  383 LYS cc_start: 0.6983 (mmmt) cc_final: 0.5545 (mmtt)
REVERT: B  462 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7778 (pt0)
REVERT: B  481 LEU cc_start: 0.8065 (tp) cc_final: 0.7100 (mt)
  outliers start: 14
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1322
  time to fit residues: 19.4150
Evaluate side-chains
  102 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.179424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.133613 restraints weight = 13673.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.59
r_work: 0.3239 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13062  Z= 0.156
  Angle     :  0.525   7.514  18458  Z= 0.280
  Chirality :  0.037   0.209   2119
  Planarity :  0.003   0.036   1666
  Dihedral  : 21.803 179.836   3799
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.71 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.26), residues: 1037
  helix:  1.25 (0.24), residues: 464
  sheet: -0.85 (0.43), residues: 155
  loop : -2.30 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 171 
 TYR   0.016   0.001   TYR A  82 
 PHE   0.012   0.001   PHE A 214 
 TRP   0.007   0.001   TRP B 443 
 HIS   0.004   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13054)
  covalent geometry    : angle       0.52406 (18455)
  hydrogen bonds       : bond        0.04204 (  525)
  hydrogen bonds       : angle       3.68839 ( 1386)
  metal coordination   : bond        0.00957 (    8)
  metal coordination   : angle       2.67581 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8622 (tptp) cc_final: 0.8363 (tptp)
REVERT: A  425 GLU cc_start: 0.7245 (tp30) cc_final: 0.6238 (pt0)
REVERT: B   98 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (tt)
REVERT: B  138 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7901 (tp30)
REVERT: B  153 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7641 (p90)
REVERT: B  462 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7720 (pt0)
REVERT: B  481 LEU cc_start: 0.7982 (tp) cc_final: 0.7021 (mt)
  outliers start: 14
  outliers final: 11
  residues processed: 104
  average time/residue: 0.1374
  time to fit residues: 19.8007
Evaluate side-chains
  104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    9.9990
   chunk 95 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 119 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0870
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.180496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134474 restraints weight = 13631.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.69
r_work: 0.3251 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13062  Z= 0.130
  Angle     :  0.516   8.302  18458  Z= 0.275
  Chirality :  0.036   0.207   2119
  Planarity :  0.003   0.036   1666
  Dihedral  : 21.799 179.591   3799
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.71 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.26), residues: 1037
  helix:  1.31 (0.24), residues: 464
  sheet: -0.81 (0.43), residues: 155
  loop : -2.28 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 171 
 TYR   0.015   0.001   TYR A  82 
 PHE   0.036   0.001   PHE A 341 
 TRP   0.007   0.001   TRP B 443 
 HIS   0.003   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (13054)
  covalent geometry    : angle       0.51499 (18455)
  hydrogen bonds       : bond        0.04110 (  525)
  hydrogen bonds       : angle       3.66836 ( 1386)
  metal coordination   : bond        0.00826 (    8)
  metal coordination   : angle       2.26285 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2942.96 seconds
wall clock time: 51 minutes 19.01 seconds (3079.01 seconds total)