Starting phenix.real_space_refine
on Wed Jul 30 15:17:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l49_23158/07_2025/7l49_23158.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l49_23158/07_2025/7l49_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l49_23158/07_2025/7l49_23158.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l49_23158/07_2025/7l49_23158.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l49_23158/07_2025/7l49_23158.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l49_23158/07_2025/7l49_23158.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:plan2': 1, ' DC%5*END:plan': 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: 7.94, per 1000 atoms: 0.64
  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: 2.97
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  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: 4.33
  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: 4.51

  Time building geometry restraints manager: 3.56 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 525 or resid 601 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:             1.050
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     34.490
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.250
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.039   0.003   TRP B 223 
 HIS   0.014   0.001   HIS A  53 
 PHE   0.026   0.002   PHE B 220 
 TYR   0.021   0.002   TYR B 113 
 ARG   0.013   0.001   ARG A  16 

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

*********************** 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  : 1.079 
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: 0.3587
  time to fit residues: 60.4699
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  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   chunk 109 optimal weight:    9.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.184369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.140270 restraints weight = 13651.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.54
r_work: 0.3326 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.139  13062  Z= 0.179
  Angle     :  0.592  10.052  18458  Z= 0.316
  Chirality :  0.038   0.201   2119
  Planarity :  0.004   0.050   1666
  Dihedral  : 21.892 174.653   3799
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.47 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.24), residues: 1037
  helix: -0.36 (0.23), residues: 458
  sheet: -1.18 (0.42), residues: 149
  loop : -2.77 (0.25), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 302 
 HIS   0.010   0.001   HIS A  53 
 PHE   0.017   0.002   PHE B 454 
 TYR   0.015   0.002   TYR B 113 
 ARG   0.004   0.001   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04604 (  525)
  hydrogen bonds       : angle       4.29745 ( 1386)
  metal coordination   : bond        0.04934 (    8)
  metal coordination   : angle       6.81645 (    3)
  covalent geometry    : bond        0.00391 (13054)
  covalent geometry    : angle       0.58584 (18455)

*********************** 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
  112 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.8741 (tptp) cc_final: 0.8272 (tmmt)
REVERT: A  438 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7454 (ttm110)
REVERT: B  276 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7942 (mmmm)
REVERT: B  343 ARG cc_start: 0.8217 (ptp-170) cc_final: 0.7770 (ptp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 112
  average time/residue: 0.3390
  time to fit residues: 50.6746
Evaluate side-chains
  102 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 SER
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 112 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 114 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 155 ASN
A 280 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 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 = 0.4083 r_free = 0.4083 target = 0.181018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137029 restraints weight = 13680.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.53
r_work: 0.3270 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  13062  Z= 0.182
  Angle     :  0.567  10.088  18458  Z= 0.302
  Chirality :  0.038   0.171   2119
  Planarity :  0.004   0.049   1666
  Dihedral  : 21.940 178.354   3799
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.69 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.25), residues: 1037
  helix:  0.42 (0.24), residues: 461
  sheet: -1.08 (0.43), residues: 155
  loop : -2.62 (0.26), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  95 
 HIS   0.007   0.001   HIS A  53 
 PHE   0.021   0.002   PHE B 205 
 TYR   0.016   0.002   TYR A  82 
 ARG   0.005   0.001   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 (  525)
  hydrogen bonds       : angle       3.98153 ( 1386)
  metal coordination   : bond        0.03188 (    8)
  metal coordination   : angle       6.05817 (    3)
  covalent geometry    : bond        0.00404 (13054)
  covalent geometry    : angle       0.56206 (18455)

*********************** 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
  125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.8681 (tptp) cc_final: 0.8446 (tptp)
REVERT: A  425 GLU cc_start: 0.7329 (tp30) cc_final: 0.6473 (pt0)
REVERT: B   98 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8065 (tt)
REVERT: B  153 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7797 (p90)
REVERT: B  343 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.7908 (ptp-170)
REVERT: B  362 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7920 (ttp-110)
REVERT: B  383 LYS cc_start: 0.6934 (tptp) cc_final: 0.6302 (mmtt)
REVERT: B  481 LEU cc_start: 0.7780 (tt) cc_final: 0.6380 (mt)
  outliers start: 15
  outliers final: 9
  residues processed: 122
  average time/residue: 0.3046
  time to fit residues: 50.7235
Evaluate side-chains
  107 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 SER
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   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  279 MET
Chi-restraints excluded: chain B residue  517 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 91 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.184098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140244 restraints weight = 13615.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.53
r_work: 0.3312 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13062  Z= 0.132
  Angle     :  0.511   7.510  18458  Z= 0.273
  Chirality :  0.036   0.156   2119
  Planarity :  0.003   0.037   1666
  Dihedral  : 21.791 179.642   3799
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.81 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.26), residues: 1037
  helix:  0.87 (0.25), residues: 462
  sheet: -0.74 (0.44), residues: 149
  loop : -2.48 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 443 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.023   0.001   PHE B 205 
 TYR   0.015   0.001   TYR B 113 
 ARG   0.003   0.000   ARG A 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04128 (  525)
  hydrogen bonds       : angle       3.76043 ( 1386)
  metal coordination   : bond        0.02127 (    8)
  metal coordination   : angle       3.62414 (    3)
  covalent geometry    : bond        0.00285 (13054)
  covalent geometry    : angle       0.50904 (18455)

*********************** 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
  122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8625 (tptp) cc_final: 0.8371 (tptp)
REVERT: A  425 GLU cc_start: 0.7314 (tp30) cc_final: 0.6431 (pt0)
REVERT: A  438 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7443 (ttm110)
REVERT: B   98 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7997 (tt)
REVERT: B  343 ARG cc_start: 0.8012 (ptp-170) cc_final: 0.7757 (ptp-170)
REVERT: B  362 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7865 (ttp-110)
REVERT: B  383 LYS cc_start: 0.7116 (tptp) cc_final: 0.6380 (mmtt)
REVERT: B  435 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8299 (m-80)
REVERT: B  481 LEU cc_start: 0.7920 (tt) cc_final: 0.6664 (mt)
  outliers start: 16
  outliers final: 11
  residues processed: 118
  average time/residue: 0.3106
  time to fit residues: 49.9927
Evaluate side-chains
  107 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
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   46 VAL
Chi-restraints excluded: chain B residue   98 ILE
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  279 MET
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  435 PHE
Chi-restraints excluded: chain B residue  517 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 114 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.181011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136751 restraints weight = 13640.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.59
r_work: 0.3257 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13062  Z= 0.173
  Angle     :  0.537   7.820  18458  Z= 0.286
  Chirality :  0.037   0.162   2119
  Planarity :  0.003   0.041   1666
  Dihedral  : 21.863 179.032   3799
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.26 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.26), residues: 1037
  helix:  0.97 (0.25), residues: 463
  sheet: -0.76 (0.43), residues: 151
  loop : -2.40 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 265 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.025   0.001   PHE B 205 
 TYR   0.018   0.001   TYR A  82 
 ARG   0.004   0.000   ARG B  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04372 (  525)
  hydrogen bonds       : angle       3.78627 ( 1386)
  metal coordination   : bond        0.01799 (    8)
  metal coordination   : angle       4.12188 (    3)
  covalent geometry    : bond        0.00386 (13054)
  covalent geometry    : angle       0.53403 (18455)

*********************** 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
  116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8655 (tptp) cc_final: 0.8399 (tptp)
REVERT: A  425 GLU cc_start: 0.7321 (tp30) cc_final: 0.6392 (pt0)
REVERT: A  438 ARG cc_start: 0.7749 (tpp-160) cc_final: 0.7428 (ttm110)
REVERT: B   98 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8029 (tt)
REVERT: B  153 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7710 (p90)
REVERT: B  383 LYS cc_start: 0.7222 (tptp) cc_final: 0.6374 (mmtt)
REVERT: B  481 LEU cc_start: 0.7857 (tt) cc_final: 0.6580 (mt)
  outliers start: 18
  outliers final: 11
  residues processed: 113
  average time/residue: 0.3009
  time to fit residues: 46.7325
Evaluate side-chains
  108 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
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  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  346 ILE
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 57 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 27 optimal weight:    0.1980
   chunk 61 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0470
   chunk 118 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 355 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 ASN
** 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 = 0.4126 r_free = 0.4126 target = 0.185203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.141094 restraints weight = 13799.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.50
r_work: 0.3332 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13062  Z= 0.121
  Angle     :  0.497   7.318  18458  Z= 0.266
  Chirality :  0.035   0.141   2119
  Planarity :  0.003   0.034   1666
  Dihedral  : 21.737 178.767   3799
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.37 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.26), residues: 1037
  helix:  1.17 (0.25), residues: 465
  sheet: -0.73 (0.43), residues: 152
  loop : -2.27 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  95 
 HIS   0.003   0.001   HIS B 353 
 PHE   0.014   0.001   PHE B 454 
 TYR   0.016   0.001   TYR B 113 
 ARG   0.004   0.000   ARG B 343 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  525)
  hydrogen bonds       : angle       3.66316 ( 1386)
  metal coordination   : bond        0.01199 (    8)
  metal coordination   : angle       2.54512 (    3)
  covalent geometry    : bond        0.00262 (13054)
  covalent geometry    : angle       0.49612 (18455)

*********************** 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
  116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8576 (tptp) cc_final: 0.8368 (tptp)
REVERT: A  425 GLU cc_start: 0.7328 (tp30) cc_final: 0.6494 (pt0)
REVERT: A  438 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7437 (ttm110)
REVERT: B   98 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7888 (tt)
REVERT: B  153 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7300 (p90)
REVERT: B  383 LYS cc_start: 0.7208 (tptp) cc_final: 0.6397 (mmtt)
REVERT: B  454 PHE cc_start: 0.8682 (t80) cc_final: 0.8481 (t80)
REVERT: B  481 LEU cc_start: 0.7890 (tt) cc_final: 0.6657 (mt)
  outliers start: 18
  outliers final: 8
  residues processed: 114
  average time/residue: 0.3346
  time to fit residues: 51.0301
Evaluate side-chains
  99 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  185 THR
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 99 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0370
   chunk 117 optimal weight:    9.9990
   chunk 90 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 109 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.5262

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.178364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.134200 restraints weight = 13724.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.54
r_work: 0.3227 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13062  Z= 0.230
  Angle     :  0.595  10.717  18458  Z= 0.313
  Chirality :  0.040   0.204   2119
  Planarity :  0.004   0.044   1666
  Dihedral  : 21.924 177.766   3799
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.15 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.26), residues: 1037
  helix:  1.02 (0.25), residues: 463
  sheet: -1.03 (0.42), residues: 160
  loop : -2.23 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 265 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.019   0.002   PHE A 214 
 TYR   0.019   0.002   TYR A  82 
 ARG   0.005   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  525)
  hydrogen bonds       : angle       3.85391 ( 1386)
  metal coordination   : bond        0.01830 (    8)
  metal coordination   : angle       4.49317 (    3)
  covalent geometry    : bond        0.00517 (13054)
  covalent geometry    : angle       0.59265 (18455)

*********************** 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
  108 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 1.823 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8652 (tptp) cc_final: 0.8380 (tptp)
REVERT: A  425 GLU cc_start: 0.7349 (tp30) cc_final: 0.6450 (pt0)
REVERT: B   98 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8106 (tt)
REVERT: B  153 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7909 (p90)
REVERT: B  383 LYS cc_start: 0.7396 (tptp) cc_final: 0.6303 (mmtt)
REVERT: B  481 LEU cc_start: 0.7990 (tt) cc_final: 0.6742 (mt)
  outliers start: 19
  outliers final: 13
  residues processed: 105
  average time/residue: 0.3586
  time to fit residues: 52.7299
Evaluate side-chains
  101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 ASP
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  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  346 ILE
Chi-restraints excluded: chain B residue  517 ILE
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 28 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 109 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 107 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4078 r_free = 0.4078 target = 0.180397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.136489 restraints weight = 13569.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.42
r_work: 0.3284 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13062  Z= 0.152
  Angle     :  0.535   9.394  18458  Z= 0.283
  Chirality :  0.037   0.204   2119
  Planarity :  0.003   0.035   1666
  Dihedral  : 21.829 179.767   3799
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.26), residues: 1037
  helix:  1.11 (0.24), residues: 465
  sheet: -0.80 (0.43), residues: 153
  loop : -2.24 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 223 
 HIS   0.003   0.001   HIS B 353 
 PHE   0.014   0.001   PHE A 205 
 TYR   0.016   0.001   TYR B 113 
 ARG   0.005   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04258 (  525)
  hydrogen bonds       : angle       3.75125 ( 1386)
  metal coordination   : bond        0.01142 (    8)
  metal coordination   : angle       2.86404 (    3)
  covalent geometry    : bond        0.00338 (13054)
  covalent geometry    : angle       0.53420 (18455)

*********************** 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
  107 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8773 (tptp) cc_final: 0.8500 (tptp)
REVERT: A  425 GLU cc_start: 0.7393 (tp30) cc_final: 0.6228 (pt0)
REVERT: A  438 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7504 (ttm110)
REVERT: B   98 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8141 (tt)
REVERT: B  153 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7673 (p90)
REVERT: B  383 LYS cc_start: 0.7414 (tptp) cc_final: 0.6288 (mmtt)
REVERT: B  454 PHE cc_start: 0.8973 (t80) cc_final: 0.8755 (t80)
REVERT: B  481 LEU cc_start: 0.7938 (tt) cc_final: 0.6765 (mt)
  outliers start: 16
  outliers final: 13
  residues processed: 104
  average time/residue: 0.4773
  time to fit residues: 69.7042
Evaluate side-chains
  104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  250 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  517 ILE
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 88 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   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 = 0.4035 r_free = 0.4035 target = 0.177014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.130740 restraints weight = 13714.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.56
r_work: 0.3212 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3533

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= 0.208
  Angle     :  0.578   8.943  18458  Z= 0.306
  Chirality :  0.039   0.213   2119
  Planarity :  0.004   0.041   1666
  Dihedral  : 21.912 178.467   3799
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.26), residues: 1037
  helix:  1.05 (0.24), residues: 464
  sheet: -1.01 (0.42), residues: 159
  loop : -2.27 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 265 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.018   0.002   PHE B 341 
 TYR   0.019   0.002   TYR A  82 
 ARG   0.004   0.000   ARG A 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04557 (  525)
  hydrogen bonds       : angle       3.84559 ( 1386)
  metal coordination   : bond        0.01506 (    8)
  metal coordination   : angle       3.78294 (    3)
  covalent geometry    : bond        0.00469 (13054)
  covalent geometry    : angle       0.57643 (18455)

*********************** 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
  105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8647 (tptp) cc_final: 0.8366 (tptp)
REVERT: A  425 GLU cc_start: 0.7362 (tp30) cc_final: 0.6337 (pt0)
REVERT: B   98 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8076 (tt)
REVERT: B  153 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7816 (p90)
REVERT: B  481 LEU cc_start: 0.7925 (tt) cc_final: 0.6775 (mt)
  outliers start: 19
  outliers final: 15
  residues processed: 101
  average time/residue: 0.2911
  time to fit residues: 40.7832
Evaluate side-chains
  103 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
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 A residue  345 SER
Chi-restraints excluded: chain A residue  421 MET
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  250 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  517 ILE
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 27 optimal weight:    0.6980
   chunk 119 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 114 optimal weight:   10.0000
   chunk 94 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:   30.0000
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 280 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 = 0.4057 r_free = 0.4057 target = 0.179149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.133529 restraints weight = 13697.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.56
r_work: 0.3246 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13062  Z= 0.158
  Angle     :  0.545   9.300  18458  Z= 0.288
  Chirality :  0.037   0.216   2119
  Planarity :  0.004   0.039   1666
  Dihedral  : 21.853 179.726   3799
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.37 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.26), residues: 1037
  helix:  1.15 (0.24), residues: 464
  sheet: -0.61 (0.44), residues: 148
  loop : -2.28 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 265 
 HIS   0.003   0.001   HIS B 353 
 PHE   0.017   0.001   PHE B 454 
 TYR   0.016   0.001   TYR A  82 
 ARG   0.006   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  525)
  hydrogen bonds       : angle       3.80649 ( 1386)
  metal coordination   : bond        0.01086 (    8)
  metal coordination   : angle       2.86016 (    3)
  covalent geometry    : bond        0.00350 (13054)
  covalent geometry    : angle       0.54385 (18455)

********************** 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
  106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 1.829 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8642 (tptp) cc_final: 0.8388 (tptp)
REVERT: A  171 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7800 (mtm180)
REVERT: A  425 GLU cc_start: 0.7253 (tp30) cc_final: 0.6260 (pt0)
REVERT: B   98 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8031 (tt)
REVERT: B  153 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7626 (p90)
REVERT: B  383 LYS cc_start: 0.7025 (mmmt) cc_final: 0.5575 (mmtt)
REVERT: B  438 ARG cc_start: 0.7270 (mmt90) cc_final: 0.6443 (mmm160)
  outliers start: 19
  outliers final: 15
  residues processed: 103
  average time/residue: 0.3868
  time to fit residues: 57.0279
Evaluate side-chains
  103 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
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 A residue  345 SER
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  250 ILE
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  517 ILE
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 65 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9990
   chunk 109 optimal weight:    9.9990
   chunk 93 optimal weight:    0.0060
   chunk 5 optimal weight:    0.0270
   chunk 62 optimal weight:    0.6980
   chunk 102 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.2852

-------------------------------------------------------------------------------
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 280 ASN
B 480 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.184418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.139469 restraints weight = 13760.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.58
r_work: 0.3325 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13062  Z= 0.112
  Angle     :  0.515  13.266  18458  Z= 0.267
  Chirality :  0.035   0.215   2119
  Planarity :  0.003   0.040   1666
  Dihedral  : 21.641 177.484   3799
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.59 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.26), residues: 1037
  helix:  1.35 (0.25), residues: 465
  sheet: -0.48 (0.45), residues: 139
  loop : -2.15 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 403 
 HIS   0.006   0.001   HIS B 480 
 PHE   0.014   0.001   PHE B 205 
 TYR   0.016   0.001   TYR B 113 
 ARG   0.005   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  525)
  hydrogen bonds       : angle       3.61716 ( 1386)
  metal coordination   : bond        0.00653 (    8)
  metal coordination   : angle       1.58226 (    3)
  covalent geometry    : bond        0.00237 (13054)
  covalent geometry    : angle       0.51508 (18455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6104.65 seconds
wall clock time: 109 minutes 35.64 seconds (6575.64 seconds total)