Starting phenix.real_space_refine
on Sat Aug 23 11:19:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l48_23157/08_2025/7l48_23157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l48_23157/08_2025/7l48_23157.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l48_23157/08_2025/7l48_23157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l48_23157/08_2025/7l48_23157.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l48_23157/08_2025/7l48_23157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l48_23157/08_2025/7l48_23157.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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     144      5.49       5
     S      37      5.16       5
     C    6739      2.51       5
     N    2052      2.21       5
     O    2512      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11488
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: "E"
      Number of atoms: 3074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 3074
          Classifications: {'RNA': 144}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 67, 'rna3p_pyr': 61}
          Link IDs: {'rna2p': 16, 'rna3p': 127}
          Chain breaks: 1
    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   3837  SG  CYS A 475      13.590  59.792  45.199  1.00144.72           S
  ATOM   4048  SG  CYS A 500      11.483  59.182  41.090  1.00168.30           S
  ATOM    364  SG  CYS A  50      53.063  98.075  78.234  1.00132.99           S
  ATOM    502  SG  CYS A  69      56.898  98.778  78.930  1.00109.77           S
  ATOM    527  SG  CYS A  72      55.165  95.811  80.252  1.00111.13           S
  ATOM   8022  SG  CYS B 475      60.243  58.550  15.167  1.00129.53           S
  ATOM   8043  SG  CYS B 478      59.669  57.064  10.831  1.00129.65           S
  ATOM   4570  SG  CYS B  50      29.666  39.470  31.268  1.00448.64           S

  Time building chain proxies: 2.79, per 1000 atoms: 0.24
  Number of scatterers: 11488
  At special positions: 0
  Unit cell: (101.85, 119.7, 111.3, 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     144     15.00
     O    2512      8.00
     N    2052      7.00
     C    6739      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: 0.81
  Conformation dependent library (CDL) restraints added in 508.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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 475 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A  53 "
        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 B 601 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 478 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 475 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B  50 "
      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:
      32 helices and 7 sheets defined
      43.8% alpha, 9.3% beta
      47 base pairs and 84 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 42
      removed outlier: 3.665A  pdb=" N   ASN A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 55
      removed outlier: 4.335A  pdb=" N   LYS A  55 " --> pdb=" O   SER A  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 51 through 55'
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 79 through 89
    Processing helix  chain 'A' and resid 94 through 126
    Processing helix  chain 'A' and resid 133 through 153
      removed outlier: 4.472A  pdb=" N   TYR A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   THR A 147 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 168
    Processing helix  chain 'A' and resid 171 through 177
      removed outlier: 3.629A  pdb=" N   LEU A 175 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 261
      removed outlier: 3.855A  pdb=" N   ARG A 261 " --> pdb=" O   GLN A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
      removed outlier: 3.597A  pdb=" N   GLU A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 367
    Processing helix  chain 'A' and resid 382 through 414
    Processing helix  chain 'A' and resid 423 through 428
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 3.857A  pdb=" N   MET A 448 " --> pdb=" O   PRO A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 493
    Processing helix  chain 'A' and resid 508 through 519
      removed outlier: 4.673A  pdb=" N   ILE A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 42
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 3.720A  pdb=" N   ALA B  57 " --> pdb=" O   HIS B  53 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 76
      removed outlier: 4.242A  pdb=" N   LYS B  73 " --> pdb=" O   CYS B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 89
    Processing helix  chain 'B' and resid 94 through 126
    Processing helix  chain 'B' and resid 133 through 144
      removed outlier: 3.831A  pdb=" N   VAL B 137 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 153
    Processing helix  chain 'B' and resid 155 through 170
      removed outlier: 3.807A  pdb=" N   ALA B 159 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.585A  pdb=" N   LEU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 281
      removed outlier: 3.998A  pdb=" N   GLY B 281 " --> pdb=" O   LYS B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 366
    Processing helix  chain 'B' and resid 382 through 415
      removed outlier: 3.954A  pdb=" N   THR B 386 " --> pdb=" O   LEU B 382 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ILE B 387 " --> pdb=" O   LYS B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 429
      removed outlier: 3.572A  pdb=" N   ARG B 429 " --> pdb=" O   GLU B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 459
    Processing helix  chain 'B' and resid 486 through 493
    Processing helix  chain 'B' and resid 510 through 518
      removed outlier: 3.743A  pdb=" N   ILE B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218
      removed outlier: 4.215A  pdb=" N   PHE A 214 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   SER A 251 " --> pdb=" O   PRO A  17 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   LEU A 253 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50
      removed outlier: 3.931A  pdb=" N   ALA A  49 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL A  64 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345
      removed outlier: 7.032A  pdb=" N   GLY A 323 " --> pdb=" O   GLN A 420 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209
      removed outlier: 3.649A  pdb=" N   TYR B 287 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259
    Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345
      removed outlier: 5.507A  pdb=" N   THR B 418 " --> pdb=" O   PRO B 319 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   GLN B 420 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   GLY B 323 " --> pdb=" O   GLN B 420 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU B 462 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 500

    365 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      114 hydrogen bonds
      216 hydrogen bond angles
      0 basepair planarities
      47 basepair parallelities
      84 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2651
        1.34 -     1.46: 3594
        1.46 -     1.58: 5439
        1.58 -     1.71: 286
        1.71 -     1.83: 51
  Bond restraints: 12021
  Sorted by residual:
  bond pdb=" CA  SER B  51 "
       pdb=" CB  SER B  51 "
    ideal  model  delta    sigma   weight residual
    1.529  1.455  0.074 1.59e-02 3.96e+03 2.17e+01
  bond pdb=" N   LYS A 383 "
       pdb=" CA  LYS A 383 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 9.20e-03 1.18e+04 1.36e+01
  bond pdb=" N   LYS B 383 "
       pdb=" CA  LYS B 383 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 9.20e-03 1.18e+04 1.30e+01
  bond pdb=" N   LEU A 194 "
       pdb=" CA  LEU A 194 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.29e-02 6.01e+03 8.79e+00
  bond pdb=" N   LEU A 382 "
       pdb=" CA  LEU A 382 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.14e-02 7.69e+03 7.94e+00
  ... (remaining 12016 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 16212
        2.23 -     4.46: 550
        4.46 -     6.69: 87
        6.69 -     8.92: 19
        8.92 -    11.15: 7
  Bond angle restraints: 16875
  Sorted by residual:
  angle pdb=" N   GLU B 390 "
        pdb=" CA  GLU B 390 "
        pdb=" CB  GLU B 390 "
      ideal   model   delta    sigma   weight residual
     110.12  118.78   -8.66 1.47e+00 4.63e-01 3.47e+01
  angle pdb=" C   PHE A 435 "
        pdb=" N   ASN A 436 "
        pdb=" CA  ASN A 436 "
      ideal   model   delta    sigma   weight residual
     121.54  132.69  -11.15 1.91e+00 2.74e-01 3.41e+01
  angle pdb=" N   GLN B  88 "
        pdb=" CA  GLN B  88 "
        pdb=" CB  GLN B  88 "
      ideal   model   delta    sigma   weight residual
     110.13  118.64   -8.51 1.48e+00 4.57e-01 3.31e+01
  angle pdb=" C   PRO B 219 "
        pdb=" N   PHE B 220 "
        pdb=" CA  PHE B 220 "
      ideal   model   delta    sigma   weight residual
     122.20  130.82   -8.62 1.72e+00 3.38e-01 2.51e+01
  angle pdb=" CA  GLU A 123 "
        pdb=" CB  GLU A 123 "
        pdb=" CG  GLU A 123 "
      ideal   model   delta    sigma   weight residual
     114.10  123.94   -9.84 2.00e+00 2.50e-01 2.42e+01
  ... (remaining 16870 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.72: 6997
       35.72 -    71.44: 426
       71.44 -   107.16: 48
      107.16 -   142.88: 2
      142.88 -   178.60: 3
  Dihedral angle restraints: 7476
    sinusoidal: 4409
      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   53.40  178.60     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   55.26  176.74     1      1.70e+01 3.46e-03 6.64e+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  -56.82 -103.18     1      1.50e+01 4.44e-03 5.24e+01
  ... (remaining 7473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1733
       0.089 -    0.179: 181
       0.179 -    0.268: 26
       0.268 -    0.357: 2
       0.357 -    0.446: 2
  Chirality restraints: 1944
  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    2.20    0.45 2.00e-01 2.50e+01 4.98e+00
  chirality pdb=" CA  CYS A  50 "
            pdb=" N   CYS A  50 "
            pdb=" C   CYS A  50 "
            pdb=" CB  CYS A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" C3'   A E 129 "
            pdb=" C4'   A E 129 "
            pdb=" O3'   A E 129 "
            pdb=" C2'   A E 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.76    0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1941 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  52 "    0.025 2.00e-02 2.50e+03   5.20e-02 2.71e+01
        pdb=" C   LYS B  52 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   LYS B  52 "    0.033 2.00e-02 2.50e+03
        pdb=" N   HIS B  53 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  48 "   -0.018 2.00e-02 2.50e+03   3.76e-02 1.41e+01
        pdb=" C   GLU B  48 "    0.065 2.00e-02 2.50e+03
        pdb=" O   GLU B  48 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ALA B  49 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  84 "    0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   LYS B  84 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   LYS B  84 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B  85 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2561
        2.79 -     3.32: 10342
        3.32 -     3.85: 21243
        3.85 -     4.37: 24108
        4.37 -     4.90: 36428
  Nonbonded interactions: 94682
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  51 "
            pdb=" CD  ARG B  66 "
     model   vdw
     2.263 3.440
  nonbonded pdb=" O   ASN A 133 "
            pdb=" OG  SER A 136 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" N6    A E 100 "
            pdb=" O2    C E 123 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OG  SER A 476 "
            pdb=" ND2 ASN A 512 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" C   SER B  51 "
            pdb=" OG  SER B  51 "
     model   vdw
     2.302 2.616
  ... (remaining 94677 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.170
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.980
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
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      :  0.008   0.692  12030  Z= 0.335
  Angle     :  0.969  11.153  16878  Z= 0.548
  Chirality :  0.058   0.446   1944
  Planarity :  0.006   0.061   1620
  Dihedral  : 20.408 178.601   5486
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.56 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.57 (0.21), residues: 1037
  helix: -1.48 (0.20), residues: 441
  sheet: -2.30 (0.40), residues: 132
  loop : -3.27 (0.22), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 363 
 TYR   0.032   0.002   TYR B 121 
 PHE   0.060   0.003   PHE A 354 
 TRP   0.035   0.003   TRP B 223 
 HIS   0.028   0.003   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12021)
  covalent geometry    : angle       0.96488 (16875)
  hydrogen bonds       : bond        0.14342 (  479)
  hydrogen bonds       : angle       6.55054 ( 1281)
  metal coordination   : bond        0.23892 (    9)
  metal coordination   : angle       6.88555 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TYR cc_start: 0.8106 (t80) cc_final: 0.7831 (t80)
REVERT: A  421 MET cc_start: 0.7801 (tmm) cc_final: 0.7521 (tmm)
REVERT: A  510 ASP cc_start: 0.8498 (m-30) cc_final: 0.8219 (m-30)
REVERT: B  353 HIS cc_start: 0.8389 (t-90) cc_final: 0.8095 (t-170)
REVERT: B  358 MET cc_start: 0.8598 (tpt) cc_final: 0.8079 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1153
  time to fit residues: 14.3858
Evaluate side-chains
  53 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0670
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    4.2126

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 HIS
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 512 ASN
A 516 ASN
A 519 ASN
B  32 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 114 ASN
B 189 ASN
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.068220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.049330 restraints weight = 63226.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.050603 restraints weight = 34506.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.051291 restraints weight = 24106.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.051746 restraints weight = 19902.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.051931 restraints weight = 17707.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  12030  Z= 0.316
  Angle     :  0.740   7.666  16878  Z= 0.392
  Chirality :  0.043   0.180   1944
  Planarity :  0.006   0.052   1620
  Dihedral  : 21.567 165.313   3334
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 20.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.47 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.24), residues: 1037
  helix: -0.17 (0.23), residues: 457
  sheet: -2.29 (0.40), residues: 141
  loop : -2.90 (0.26), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 343 
 TYR   0.018   0.003   TYR A 434 
 PHE   0.024   0.002   PHE B 220 
 TRP   0.014   0.002   TRP B 443 
 HIS   0.009   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 (12021)
  covalent geometry    : angle       0.73780 (16875)
  hydrogen bonds       : bond        0.05924 (  479)
  hydrogen bonds       : angle       4.97368 ( 1281)
  metal coordination   : bond        0.02025 (    9)
  metal coordination   : angle       4.33310 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 PHE cc_start: 0.8604 (t80) cc_final: 0.8345 (t80)
REVERT: A  357 LYS cc_start: 0.9174 (pptt) cc_final: 0.8943 (pptt)
REVERT: A  510 ASP cc_start: 0.8715 (m-30) cc_final: 0.8355 (m-30)
REVERT: B  353 HIS cc_start: 0.8911 (t-90) cc_final: 0.8466 (t-170)
REVERT: B  421 MET cc_start: 0.6952 (tmm) cc_final: 0.6735 (tmm)
  outliers start: 19
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1250
  time to fit residues: 13.7303
Evaluate side-chains
  57 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  232 TYR
Chi-restraints excluded: chain B residue  489 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 115 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 104 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 169 ASN
A 210 HIS
A 512 ASN
A 516 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.070735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.051133 restraints weight = 62409.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.052549 restraints weight = 32524.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.053282 restraints weight = 22110.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.053796 restraints weight = 18001.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.054025 restraints weight = 15846.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12030  Z= 0.144
  Angle     :  0.585   6.523  16878  Z= 0.306
  Chirality :  0.038   0.167   1944
  Planarity :  0.004   0.039   1620
  Dihedral  : 21.427 168.681   3334
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.37 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.25), residues: 1037
  helix:  0.43 (0.23), residues: 461
  sheet: -2.11 (0.41), residues: 143
  loop : -2.75 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 440 
 TYR   0.015   0.002   TYR A 202 
 PHE   0.022   0.001   PHE A 341 
 TRP   0.012   0.001   TRP B 223 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (12021)
  covalent geometry    : angle       0.58437 (16875)
  hydrogen bonds       : bond        0.04774 (  479)
  hydrogen bonds       : angle       4.44708 ( 1281)
  metal coordination   : bond        0.00682 (    9)
  metal coordination   : angle       1.89042 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7808 (tpp)
REVERT: A  346 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6123 (mp)
REVERT: A  354 PHE cc_start: 0.8718 (t80) cc_final: 0.8000 (t80)
REVERT: A  448 MET cc_start: 0.7680 (ttp) cc_final: 0.7372 (ptm)
REVERT: A  510 ASP cc_start: 0.8472 (m-30) cc_final: 0.8184 (m-30)
REVERT: B  353 HIS cc_start: 0.9017 (t-90) cc_final: 0.8748 (t-170)
REVERT: B  421 MET cc_start: 0.7071 (tmm) cc_final: 0.6690 (tmm)
  outliers start: 20
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1036
  time to fit residues: 11.1742
Evaluate side-chains
  63 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  489 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 93 optimal weight:    0.0270
   chunk 78 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 105 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    4.8046

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
A 338 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.066451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.047232 restraints weight = 65254.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.048550 restraints weight = 33852.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.049294 restraints weight = 23125.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.049653 restraints weight = 18768.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.049915 restraints weight = 16913.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.099  12030  Z= 0.340
  Angle     :  0.752   8.017  16878  Z= 0.395
  Chirality :  0.043   0.193   1944
  Planarity :  0.005   0.057   1620
  Dihedral  : 21.830 167.084   3334
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 23.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.04 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.25), residues: 1037
  helix:  0.40 (0.23), residues: 453
  sheet: -2.18 (0.42), residues: 143
  loop : -2.72 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 438 
 TYR   0.018   0.002   TYR B 445 
 PHE   0.022   0.002   PHE B 495 
 TRP   0.012   0.002   TRP A 223 
 HIS   0.005   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (12021)
  covalent geometry    : angle       0.75070 (16875)
  hydrogen bonds       : bond        0.06177 (  479)
  hydrogen bonds       : angle       4.91884 ( 1281)
  metal coordination   : bond        0.02519 (    9)
  metal coordination   : angle       3.35878 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 44
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  346 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6668 (mp)
REVERT: A  354 PHE cc_start: 0.8760 (t80) cc_final: 0.8288 (t80)
REVERT: A  510 ASP cc_start: 0.8767 (m-30) cc_final: 0.8371 (m-30)
REVERT: B  421 MET cc_start: 0.7429 (tmm) cc_final: 0.7065 (tmm)
  outliers start: 28
  outliers final: 16
  residues processed: 66
  average time/residue: 0.0918
  time to fit residues: 9.4043
Evaluate side-chains
  57 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  435 PHE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  489 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   chunk 110 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.067428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.048168 restraints weight = 63866.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.049513 restraints weight = 32976.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.050272 restraints weight = 22459.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.050684 restraints weight = 18169.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.050807 restraints weight = 16218.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  12030  Z= 0.244
  Angle     :  0.653   8.102  16878  Z= 0.341
  Chirality :  0.040   0.165   1944
  Planarity :  0.004   0.038   1620
  Dihedral  : 21.710 167.713   3334
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 18.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.26 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.04 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.26), residues: 1037
  helix:  0.67 (0.23), residues: 457
  sheet: -2.07 (0.43), residues: 142
  loop : -2.54 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 438 
 TYR   0.016   0.002   TYR B 445 
 PHE   0.015   0.002   PHE B 495 
 TRP   0.012   0.001   TRP A 223 
 HIS   0.003   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (12021)
  covalent geometry    : angle       0.65235 (16875)
  hydrogen bonds       : bond        0.05334 (  479)
  hydrogen bonds       : angle       4.64968 ( 1281)
  metal coordination   : bond        0.01726 (    9)
  metal coordination   : angle       2.29693 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 TYR cc_start: 0.8828 (t80) cc_final: 0.8230 (t80)
REVERT: A  346 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6827 (mp)
REVERT: A  510 ASP cc_start: 0.8688 (m-30) cc_final: 0.8304 (m-30)
  outliers start: 24
  outliers final: 17
  residues processed: 69
  average time/residue: 0.0893
  time to fit residues: 9.8061
Evaluate side-chains
  60 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  489 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 112 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
A 369 ASN
A 512 ASN
A 516 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.069481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.050065 restraints weight = 63097.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.051469 restraints weight = 32337.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.052228 restraints weight = 21840.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.052674 restraints weight = 17650.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.052866 restraints weight = 15705.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12030  Z= 0.143
  Angle     :  0.584   9.539  16878  Z= 0.300
  Chirality :  0.037   0.174   1944
  Planarity :  0.004   0.035   1620
  Dihedral  : 21.423 168.556   3334
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.93 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.21 (0.26), residues: 1037
  helix:  0.93 (0.24), residues: 468
  sheet: -1.82 (0.44), residues: 142
  loop : -2.47 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  34 
 TYR   0.013   0.001   TYR A  82 
 PHE   0.011   0.001   PHE A 341 
 TRP   0.011   0.001   TRP B 223 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (12021)
  covalent geometry    : angle       0.58352 (16875)
  hydrogen bonds       : bond        0.04692 (  479)
  hydrogen bonds       : angle       4.29789 ( 1281)
  metal coordination   : bond        0.00755 (    9)
  metal coordination   : angle       1.44543 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 57
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TYR cc_start: 0.8814 (t80) cc_final: 0.8213 (t80)
REVERT: A  317 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7969 (p)
REVERT: A  510 ASP cc_start: 0.8482 (m-30) cc_final: 0.8246 (m-30)
REVERT: B   78 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7952 (t70)
REVERT: B  358 MET cc_start: 0.8704 (tpp) cc_final: 0.8497 (tpp)
  outliers start: 27
  outliers final: 19
  residues processed: 80
  average time/residue: 0.0966
  time to fit residues: 11.8021
Evaluate side-chains
  69 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  489 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 112 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
A 210 HIS
A 512 ASN
A 516 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 516 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.070573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.051196 restraints weight = 62702.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.052607 restraints weight = 32149.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.053388 restraints weight = 21655.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.053862 restraints weight = 17458.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.054046 restraints weight = 15470.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12030  Z= 0.120
  Angle     :  0.595  11.195  16878  Z= 0.299
  Chirality :  0.037   0.200   1944
  Planarity :  0.004   0.038   1620
  Dihedral  : 21.219 168.472   3334
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.71 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.26), residues: 1037
  helix:  1.17 (0.24), residues: 461
  sheet: -1.69 (0.44), residues: 143
  loop : -2.43 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 361 
 TYR   0.012   0.001   TYR A  82 
 PHE   0.024   0.001   PHE A 498 
 TRP   0.012   0.001   TRP B 223 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (12021)
  covalent geometry    : angle       0.59451 (16875)
  hydrogen bonds       : bond        0.04506 (  479)
  hydrogen bonds       : angle       4.20732 ( 1281)
  metal coordination   : bond        0.00564 (    9)
  metal coordination   : angle       1.27200 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TYR cc_start: 0.8837 (t80) cc_final: 0.8299 (t80)
REVERT: A  178 MET cc_start: 0.8414 (ttt) cc_final: 0.7863 (tpp)
REVERT: A  510 ASP cc_start: 0.8357 (m-30) cc_final: 0.8098 (m-30)
REVERT: B   78 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7941 (t70)
REVERT: B  358 MET cc_start: 0.8729 (tpp) cc_final: 0.8431 (tpp)
REVERT: B  427 MET cc_start: 0.8688 (ttp) cc_final: 0.8344 (tmm)
  outliers start: 20
  outliers final: 13
  residues processed: 77
  average time/residue: 0.1059
  time to fit residues: 12.2900
Evaluate side-chains
  64 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  387 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 66 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 210 HIS
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.070431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.050900 restraints weight = 62526.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.052316 restraints weight = 32136.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.053117 restraints weight = 21762.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.053470 restraints weight = 17495.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.053758 restraints weight = 15816.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12030  Z= 0.137
  Angle     :  0.594  11.773  16878  Z= 0.300
  Chirality :  0.037   0.170   1944
  Planarity :  0.004   0.039   1620
  Dihedral  : 21.156 168.743   3334
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.82 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.27), residues: 1037
  helix:  1.29 (0.24), residues: 460
  sheet: -1.59 (0.44), residues: 143
  loop : -2.38 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 361 
 TYR   0.011   0.001   TYR A  82 
 PHE   0.021   0.001   PHE A 214 
 TRP   0.009   0.001   TRP B 223 
 HIS   0.004   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12021)
  covalent geometry    : angle       0.59404 (16875)
  hydrogen bonds       : bond        0.04546 (  479)
  hydrogen bonds       : angle       4.20423 ( 1281)
  metal coordination   : bond        0.00795 (    9)
  metal coordination   : angle       1.47137 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TYR cc_start: 0.8850 (t80) cc_final: 0.8285 (t80)
REVERT: A  178 MET cc_start: 0.8359 (ttt) cc_final: 0.7858 (tpp)
REVERT: A  317 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7924 (p)
REVERT: A  354 PHE cc_start: 0.8705 (t80) cc_final: 0.7794 (t80)
REVERT: A  448 MET cc_start: 0.8420 (ptm) cc_final: 0.8124 (ptm)
REVERT: A  510 ASP cc_start: 0.8378 (m-30) cc_final: 0.8126 (m-30)
REVERT: B   78 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7885 (t70)
REVERT: B  358 MET cc_start: 0.8741 (tpp) cc_final: 0.8432 (tpp)
REVERT: B  427 MET cc_start: 0.8703 (ttp) cc_final: 0.8359 (tmm)
  outliers start: 26
  outliers final: 18
  residues processed: 73
  average time/residue: 0.1000
  time to fit residues: 10.9636
Evaluate side-chains
  69 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 49
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  163 ARG
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  387 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 68 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 95 optimal weight:    0.9990
   chunk 57 optimal weight:    0.4980
   chunk 89 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 210 HIS
A 512 ASN
A 516 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.071539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.052298 restraints weight = 62947.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.053724 restraints weight = 32203.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.054542 restraints weight = 21714.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.054923 restraints weight = 17371.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.055200 restraints weight = 15648.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12030  Z= 0.114
  Angle     :  0.594  12.655  16878  Z= 0.299
  Chirality :  0.037   0.175   1944
  Planarity :  0.004   0.039   1620
  Dihedral  : 21.029 169.124   3334
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.16 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.27), residues: 1037
  helix:  1.30 (0.24), residues: 462
  sheet: -1.59 (0.44), residues: 143
  loop : -2.30 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 361 
 TYR   0.011   0.001   TYR A 113 
 PHE   0.015   0.001   PHE A 214 
 TRP   0.012   0.001   TRP B 302 
 HIS   0.004   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (12021)
  covalent geometry    : angle       0.59383 (16875)
  hydrogen bonds       : bond        0.04403 (  479)
  hydrogen bonds       : angle       4.09817 ( 1281)
  metal coordination   : bond        0.00374 (    9)
  metal coordination   : angle       1.07308 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.5938 (m-10)
REVERT: A  121 TYR cc_start: 0.8825 (t80) cc_final: 0.8309 (t80)
REVERT: A  178 MET cc_start: 0.8191 (ttt) cc_final: 0.7765 (tpp)
REVERT: A  317 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7810 (p)
REVERT: A  354 PHE cc_start: 0.8473 (t80) cc_final: 0.7905 (t80)
REVERT: A  510 ASP cc_start: 0.8302 (m-30) cc_final: 0.8067 (m-30)
REVERT: B   78 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7864 (t70)
REVERT: B  358 MET cc_start: 0.8762 (tpp) cc_final: 0.8452 (tpp)
  outliers start: 21
  outliers final: 16
  residues processed: 74
  average time/residue: 0.1034
  time to fit residues: 11.5414
Evaluate side-chains
  70 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 51
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  163 ARG
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  387 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0770
   chunk 18 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 112 optimal weight:   10.0000
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
B 305 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.071607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.052279 restraints weight = 63711.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.053702 restraints weight = 32537.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 71)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.054486 restraints weight = 22011.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.054918 restraints weight = 17679.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.055121 restraints weight = 15756.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12030  Z= 0.114
  Angle     :  0.610  12.809  16878  Z= 0.305
  Chirality :  0.037   0.231   1944
  Planarity :  0.004   0.041   1620
  Dihedral  : 20.913 168.376   3334
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.60 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.27), residues: 1037
  helix:  1.38 (0.25), residues: 456
  sheet: -1.69 (0.43), residues: 144
  loop : -2.24 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  34 
 TYR   0.010   0.001   TYR A 113 
 PHE   0.019   0.001   PHE A 498 
 TRP   0.011   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12021)
  covalent geometry    : angle       0.61016 (16875)
  hydrogen bonds       : bond        0.04449 (  479)
  hydrogen bonds       : angle       4.05643 ( 1281)
  metal coordination   : bond        0.00494 (    9)
  metal coordination   : angle       1.15490 (    3)

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

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6025 (m-10)
REVERT: A  121 TYR cc_start: 0.8867 (t80) cc_final: 0.8342 (t80)
REVERT: A  178 MET cc_start: 0.8097 (ttt) cc_final: 0.7541 (tpp)
REVERT: A  317 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7810 (p)
REVERT: A  354 PHE cc_start: 0.8394 (t80) cc_final: 0.8092 (t80)
REVERT: A  510 ASP cc_start: 0.8404 (m-30) cc_final: 0.8112 (m-30)
REVERT: B   78 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7878 (t70)
REVERT: B  303 MET cc_start: 0.2216 (tmm) cc_final: 0.1636 (tmm)
REVERT: B  358 MET cc_start: 0.8775 (tpp) cc_final: 0.8418 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1004
  time to fit residues: 11.5119
Evaluate side-chains
  71 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 50
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   59 TYR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  352 PHE
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  163 ARG
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  387 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 84 optimal weight:    0.0770
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 94 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.8542

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
A 512 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.071746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.052303 restraints weight = 64542.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.053737 restraints weight = 33078.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.054554 restraints weight = 22431.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.055001 restraints weight = 18034.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.055192 restraints weight = 16015.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12030  Z= 0.116
  Angle     :  0.604  12.716  16878  Z= 0.304
  Chirality :  0.037   0.223   1944
  Planarity :  0.004   0.040   1620
  Dihedral  : 20.830 167.958   3334
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 21.71 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.27), residues: 1037
  helix:  1.37 (0.25), residues: 456
  sheet: -1.77 (0.43), residues: 146
  loop : -2.17 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  34 
 TYR   0.044   0.001   TYR A 140 
 PHE   0.013   0.001   PHE A 359 
 TRP   0.011   0.001   TRP A 403 
 HIS   0.005   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12021)
  covalent geometry    : angle       0.60412 (16875)
  hydrogen bonds       : bond        0.04354 (  479)
  hydrogen bonds       : angle       4.06412 ( 1281)
  metal coordination   : bond        0.00618 (    9)
  metal coordination   : angle       1.20775 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2023.76 seconds
wall clock time: 35 minutes 57.37 seconds (2157.37 seconds total)