Starting phenix.real_space_refine
on Thu Jan 18 06:50:45 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/01_2024/7uxa_26856.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/01_2024/7uxa_26856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/01_2024/7uxa_26856.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/01_2024/7uxa_26856.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/01_2024/7uxa_26856.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/01_2024/7uxa_26856.pdb"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
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
     P      77      5.49       5
     Mg      2      5.21       5
     S      26      5.16       5
     C    4890      2.51       5
     N    1420      2.21       5
     O    1705      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  139": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  306": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 8120
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1762
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 212}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 971
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1615
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 191}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 2105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2105
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 16, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "E"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 1667
          Unusual residues: {' MG': 2}
          Inner-chain residues flagged as termini: ['pdbres="  A E  47 "']
          Classifications: {'RNA': 78, 'undetermined': 2}
          Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 13, 'rna3p': 64, None: 2}
            Not linked:
              pdbres="  G E  88 "
              pdbres=" MG E 101 "
            Not linked:
              pdbres=" MG E 101 "
              pdbres=" MG E 102 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 5.15, per 1000 atoms: 0.63
  Number of scatterers: 8120
  At special positions: 0
  Unit cell: (87.608, 86.676, 123.024, 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)
     S      26     16.00
     P      77     15.00
     Mg      2     11.99
     O    1705      8.00
     N    1420      7.00
     C    4890      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  - 3.50
        Amino acid           : False - 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: 3.32
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1530

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      35.4% alpha, 16.3% beta
      27 base pairs and 38 stacking pairs defined.
    Time for finding SS restraints: 2.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 25
    Processing helix  chain 'A' and resid 53 through 63
    Processing helix  chain 'A' and resid 83 through 101
      removed outlier: 3.593A  pdb=" N   GLN A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLU A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 230
      removed outlier: 3.608A  pdb=" N   ASP A 226 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
    Processing helix  chain 'A' and resid 270 through 285
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 4.314A  pdb=" N   GLU B  48 " --> pdb=" O   PRO B  44 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASP B  53 " --> pdb=" O   MET B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 73
    Processing helix  chain 'B' and resid 116 through 131
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 300 through 310
    Processing helix  chain 'C' and resid 324 through 336
    Processing helix  chain 'C' and resid 338 through 349
    Processing helix  chain 'C' and resid 400 through 414
    Processing helix  chain 'C' and resid 430 through 443
      removed outlier: 3.824A  pdb=" N   GLU C 435 " --> pdb=" O   LYS C 432 " (cutoff:3.500A)
      Proline residue:  C 437  - end of helix
      removed outlier: 3.622A  pdb=" N   ILE C 443 " --> pdb=" O   MET C 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 27
      removed outlier: 3.851A  pdb=" N   ARG D  27 " --> pdb=" O   LEU D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 67
      removed outlier: 3.707A  pdb=" N   ALA D  52 " --> pdb=" O   SER D  48 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLU D  53 " --> pdb=" O   ALA D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 77
      No H-bonds generated for 'chain 'D' and resid 75 through 77'
    Processing helix  chain 'D' and resid 96 through 101
      removed outlier: 3.611A  pdb=" N   THR D 101 " --> pdb=" O   PHE D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 124
    Processing helix  chain 'D' and resid 136 through 145
      removed outlier: 3.673A  pdb=" N   LEU D 145 " --> pdb=" O   TYR D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 163
    Processing helix  chain 'D' and resid 454 through 459
      removed outlier: 3.842A  pdb=" N   ALA D 459 " --> pdb=" O   ASP D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 484 through 495
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32
      removed outlier: 4.512A  pdb=" N   SER A  11 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU A   2 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   VAL A  69 " --> pdb=" O   LEU A   2 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   VAL A   4 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.524A  pdb=" N   GLU D  72 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ARG D  70 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235
      removed outlier: 4.610A  pdb=" N   LEU A 289 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   CYS A 291 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 235
      removed outlier: 4.610A  pdb=" N   LEU A 289 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   CYS A 291 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 288 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR B 104 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   ALA B 142 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   VAL B 106 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   VAL B 144 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   THR B 108 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ILE B  90 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 269
      removed outlier: 4.115A  pdb=" N   LEU B 114 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 297 through 299
      removed outlier: 3.850A  pdb=" N   VAL C  49 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   PHE C  40 " --> pdb=" O   SER C 315 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TYR C 317 " --> pdb=" O   PHE C  40 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ALA C  42 " --> pdb=" O   TYR C 317 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358
      removed outlier: 4.025A  pdb=" N   TYR C 380 " --> pdb=" O   LEU C 368 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 387
      removed outlier: 3.540A  pdb=" N   LEU C 423 " --> pdb=" O   GLU C 385 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   GLU C 447 " --> pdb=" O   PHE D 518 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   CYS D 474 " --> pdb=" O   ALA D 503 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   VAL D 505 " --> pdb=" O   CYS D 474 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   SER D 476 " --> pdb=" O   VAL D 505 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 104 through 106

    264 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      68 hydrogen bonds
      110 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      38 stacking parallelities
  Total time for adding SS restraints: 2.54

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2137
        1.33 -     1.45: 1945
        1.45 -     1.57: 4193
        1.57 -     1.69: 153
        1.69 -     1.81: 41
  Bond restraints: 8469
  Sorted by residual:
  bond pdb=" CA  GLY B  94 "
       pdb=" C   GLY B  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.511  0.011 1.13e-02 7.83e+03 8.78e-01
  bond pdb=" CB  TRP D  99 "
       pdb=" CG  TRP D  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.02e-01
  bond pdb=" CA  ALA A 286 "
       pdb=" C   ALA A 286 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.009 1.08e-02 8.57e+03 6.87e-01
  bond pdb=" CA  ALA C 377 "
       pdb=" C   ALA C 377 "
    ideal  model  delta    sigma   weight residual
    1.531  1.522  0.009 1.12e-02 7.97e+03 6.49e-01
  bond pdb=" CA  GLU C 458 "
       pdb=" C   GLU C 458 "
    ideal  model  delta    sigma   weight residual
    1.530  1.521  0.009 1.10e-02 8.26e+03 6.09e-01
  ... (remaining 8464 not shown)

  Histogram of bond angle deviations from ideal:
      100.31 -   107.06: 709
      107.06 -   113.80: 4830
      113.80 -   120.55: 3241
      120.55 -   127.30: 2852
      127.30 -   134.05: 237
  Bond angle restraints: 11869
  Sorted by residual:
  angle pdb=" N   ASP A 243 "
        pdb=" CA  ASP A 243 "
        pdb=" C   ASP A 243 "
      ideal   model   delta    sigma   weight residual
     114.75  111.06    3.69 1.26e+00 6.30e-01 8.60e+00
  angle pdb=" N   THR D 429 "
        pdb=" CA  THR D 429 "
        pdb=" C   THR D 429 "
      ideal   model   delta    sigma   weight residual
     107.23  111.62   -4.39 1.67e+00 3.59e-01 6.92e+00
  angle pdb=" N   LYS C 371 "
        pdb=" CA  LYS C 371 "
        pdb=" C   LYS C 371 "
      ideal   model   delta    sigma   weight residual
     108.19  111.38   -3.19 1.29e+00 6.01e-01 6.13e+00
  angle pdb=" N   TYR C 362 "
        pdb=" CA  TYR C 362 "
        pdb=" C   TYR C 362 "
      ideal   model   delta    sigma   weight residual
     109.65  105.95    3.70 1.56e+00 4.11e-01 5.64e+00
  angle pdb=" N   VAL C 335 "
        pdb=" CA  VAL C 335 "
        pdb=" C   VAL C 335 "
      ideal   model   delta    sigma   weight residual
     113.07  110.04    3.03 1.36e+00 5.41e-01 4.97e+00
  ... (remaining 11864 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.49: 4795
       24.49 -    48.98: 176
       48.98 -    73.47: 117
       73.47 -    97.97: 11
       97.97 -   122.46: 3
  Dihedral angle restraints: 5102
    sinusoidal: 2729
      harmonic: 2373
  Sorted by residual:
  dihedral pdb=" CA  LEU C 360 "
           pdb=" C   LEU C 360 "
           pdb=" N   LYS C 361 "
           pdb=" CA  LYS C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.82   20.18     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" O4'   G E  72 "
           pdb=" C1'   G E  72 "
           pdb=" N9    G E  72 "
           pdb=" C4    G E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -19.43  -70.57     1      2.00e+01 2.50e-03 1.60e+01
  dihedral pdb=" O4'   A E  52 "
           pdb=" C1'   A E  52 "
           pdb=" N9    A E  52 "
           pdb=" C4    A E  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -158.89   52.89     1      1.70e+01 3.46e-03 1.32e+01
  ... (remaining 5099 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1053
       0.037 -    0.074: 249
       0.074 -    0.111: 69
       0.111 -    0.147: 12
       0.147 -    0.184: 1
  Chirality restraints: 1384
  Sorted by residual:
  chirality pdb=" C1'   A E  74 "
            pdb=" O4'   A E  74 "
            pdb=" C2'   A E  74 "
            pdb=" N9    A E  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.27    0.18 2.00e-01 2.50e+01 8.48e-01
  chirality pdb=" C1'   G E  22 "
            pdb=" O4'   G E  22 "
            pdb=" C2'   G E  22 "
            pdb=" N9    G E  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE B  90 "
            pdb=" N   ILE B  90 "
            pdb=" C   ILE B  90 "
            pdb=" CB  ILE B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 1381 not shown)

  Planarity restraints: 1229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 373 "   -0.036 5.00e-02 4.00e+02   5.36e-02 4.60e+00
        pdb=" N   PRO C 374 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 374 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 374 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  74 "    0.024 2.00e-02 2.50e+03   1.10e-02 3.32e+00
        pdb=" N9    A E  74 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8    A E  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A E  74 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A E  74 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A E  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A E  74 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A E  74 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U E   6 "   -0.020 2.00e-02 2.50e+03   1.08e-02 2.61e+00
        pdb=" N1    U E   6 "    0.024 2.00e-02 2.50e+03
        pdb=" C2    U E   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U E   6 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U E   6 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    U E   6 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4    U E   6 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    U E   6 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U E   6 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1226 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 142
        2.65 -     3.21: 7217
        3.21 -     3.77: 13257
        3.77 -     4.34: 17916
        4.34 -     4.90: 28118
  Nonbonded interactions: 66650
  Sorted by model distance:
  nonbonded pdb=" OP1   G E   9 "
            pdb="MG    MG E 101 "
     model   vdw
     2.084 2.170
  nonbonded pdb=" OG  SER D 495 "
            pdb=" O   VAL D 498 "
     model   vdw
     2.168 2.440
  nonbonded pdb=" OE1 GLU A  62 "
            pdb=" OH  TYR A 221 "
     model   vdw
     2.199 2.440
  nonbonded pdb=" NH2 ARG D  27 "
            pdb=" OP1   G E  17 "
     model   vdw
     2.252 2.520
  nonbonded pdb=" OE1 GLU D 122 "
            pdb=" OH  TYR D 155 "
     model   vdw
     2.255 2.440
  ... (remaining 66645 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.830
  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:          7.170
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     26.780
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
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      :  0.003   0.028   8469  Z= 0.221
  Angle     :  0.577   5.955  11869  Z= 0.330
  Chirality :  0.036   0.184   1384
  Planarity :  0.004   0.054   1229
  Dihedral  : 16.038 122.458   3572
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.00 %
    Favored  : 93.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.31), residues: 805
  helix:  0.29 (0.31), residues: 276
  sheet: -1.95 (0.45), residues: 128
  loop : -0.75 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  99 
 HIS   0.003   0.001   HIS A 211 
 PHE   0.013   0.001   PHE A 244 
 TYR   0.010   0.001   TYR D 155 
 ARG   0.003   0.000   ARG A 220 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7116 (mtp180)
REVERT: B   59 GLN cc_start: 0.8097 (mt0) cc_final: 0.7868 (mp10)
REVERT: B   81 CYS cc_start: 0.9034 (m) cc_final: 0.8592 (p)
REVERT: B  147 ASP cc_start: 0.8943 (t0) cc_final: 0.8663 (t0)
REVERT: B  161 LEU cc_start: 0.8177 (mt) cc_final: 0.7880 (pt)
REVERT: C   46 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (m-40)
REVERT: C   58 GLU cc_start: 0.5999 (mt-10) cc_final: 0.4964 (tp30)
REVERT: C  317 TYR cc_start: 0.6729 (m-80) cc_final: 0.6519 (m-80)
REVERT: C  367 LEU cc_start: 0.8298 (mt) cc_final: 0.7883 (mp)
REVERT: C  429 MET cc_start: 0.6062 (tmm) cc_final: 0.5803 (tmm)
  outliers start: 6
  outliers final: 1
  residues processed: 161
  average time/residue: 0.2256
  time to fit residues: 48.5788
Evaluate side-chains
  106 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 ASN
Chi-restraints excluded: chain C residue  447 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.0040
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0670
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5732

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 413 ASN
** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 464 ASN
D 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8469  Z= 0.165
  Angle     :  0.500   5.691  11869  Z= 0.257
  Chirality :  0.037   0.169   1384
  Planarity :  0.004   0.050   1229
  Dihedral  : 17.872 119.068   2045
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.42 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.31), residues: 805
  helix:  0.83 (0.32), residues: 272
  sheet: -1.49 (0.45), residues: 132
  loop : -0.51 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  99 
 HIS   0.002   0.001   HIS B  77 
 PHE   0.012   0.001   PHE A  86 
 TYR   0.017   0.001   TYR B  67 
 ARG   0.009   0.000   ARG C 340 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.7075 (mtp180)
REVERT: B  161 LEU cc_start: 0.8160 (mt) cc_final: 0.7840 (pt)
REVERT: C   44 MET cc_start: 0.8042 (tpp) cc_final: 0.7498 (tpt)
REVERT: C  348 TYR cc_start: 0.7217 (t80) cc_final: 0.6965 (t80)
REVERT: C  367 LEU cc_start: 0.8103 (mt) cc_final: 0.7719 (mp)
REVERT: C  413 ASN cc_start: 0.8013 (m-40) cc_final: 0.7771 (m110)
REVERT: C  429 MET cc_start: 0.6078 (tmm) cc_final: 0.5843 (tmm)
REVERT: C  434 MET cc_start: 0.5671 (mmt) cc_final: 0.5451 (mmt)
REVERT: D   90 GLU cc_start: 0.8410 (tt0) cc_final: 0.8114 (pt0)
REVERT: D  460 THR cc_start: 0.9291 (p) cc_final: 0.8908 (t)
REVERT: D  465 ASN cc_start: 0.8262 (p0) cc_final: 0.8020 (p0)
REVERT: D  509 ASP cc_start: 0.8488 (t0) cc_final: 0.8228 (t70)
  outliers start: 11
  outliers final: 5
  residues processed: 120
  average time/residue: 0.2258
  time to fit residues: 35.9817
Evaluate side-chains
  107 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  519 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A  43 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN
C  59 GLN
** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 GLN
D 156 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8469  Z= 0.230
  Angle     :  0.524   5.633  11869  Z= 0.267
  Chirality :  0.038   0.170   1384
  Planarity :  0.004   0.049   1229
  Dihedral  : 17.714 116.384   2040
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.74 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.31), residues: 805
  helix:  0.94 (0.31), residues: 272
  sheet: -1.39 (0.45), residues: 134
  loop : -0.46 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  63 
 HIS   0.002   0.001   HIS A 211 
 PHE   0.010   0.001   PHE A 244 
 TYR   0.016   0.002   TYR B  67 
 ARG   0.008   0.000   ARG A 214 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A   10 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7114 (mtp180)
REVERT: A  205 GLN cc_start: 0.6688 (tm-30) cc_final: 0.6131 (tm-30)
REVERT: B   59 GLN cc_start: 0.8233 (mp10) cc_final: 0.7961 (mp10)
REVERT: B   89 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7967 (mp)
REVERT: B  161 LEU cc_start: 0.8204 (mt) cc_final: 0.7860 (pt)
REVERT: C   44 MET cc_start: 0.7746 (tpp) cc_final: 0.7481 (tpt)
REVERT: C   68 LYS cc_start: 0.6563 (tttt) cc_final: 0.6363 (ttpp)
REVERT: C  348 TYR cc_start: 0.7777 (t80) cc_final: 0.7291 (t80)
REVERT: D   90 GLU cc_start: 0.8462 (tt0) cc_final: 0.8051 (pm20)
REVERT: D  460 THR cc_start: 0.9299 (p) cc_final: 0.8920 (t)
REVERT: D  465 ASN cc_start: 0.8550 (p0) cc_final: 0.8270 (p0)
  outliers start: 14
  outliers final: 8
  residues processed: 115
  average time/residue: 0.1944
  time to fit residues: 31.0458
Evaluate side-chains
  104 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0570
   chunk 38 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0040
   chunk 23 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.4116

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A  78 HIS
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN
D  35 GLN
D 156 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8469  Z= 0.294
  Angle     :  0.552   5.704  11869  Z= 0.282
  Chirality :  0.038   0.178   1384
  Planarity :  0.004   0.049   1229
  Dihedral  : 17.747 117.672   2040
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.76 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.31), residues: 805
  helix:  0.91 (0.31), residues: 272
  sheet: -1.69 (0.44), residues: 146
  loop : -0.40 (0.35), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  63 
 HIS   0.002   0.001   HIS A  79 
 PHE   0.011   0.002   PHE A 244 
 TYR   0.014   0.002   TYR D 155 
 ARG   0.005   0.001   ARG A 214 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7655 (mmt-90) cc_final: 0.7149 (mtp180)
REVERT: A  205 GLN cc_start: 0.6716 (tm-30) cc_final: 0.6135 (tm-30)
REVERT: B   40 MET cc_start: 0.6263 (mtp) cc_final: 0.5759 (mtp)
REVERT: B   59 GLN cc_start: 0.8341 (mp10) cc_final: 0.7841 (mp10)
REVERT: B   89 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8101 (mp)
REVERT: B  161 LEU cc_start: 0.8210 (mt) cc_final: 0.7833 (pt)
REVERT: C   44 MET cc_start: 0.7801 (tpp) cc_final: 0.7553 (tpt)
REVERT: C   68 LYS cc_start: 0.6635 (tttt) cc_final: 0.6220 (ttpp)
REVERT: C  348 TYR cc_start: 0.7889 (t80) cc_final: 0.7363 (t80)
REVERT: D   63 TRP cc_start: 0.8571 (m100) cc_final: 0.8340 (m100)
REVERT: D   90 GLU cc_start: 0.8473 (tt0) cc_final: 0.8179 (pm20)
REVERT: D  460 THR cc_start: 0.9308 (p) cc_final: 0.8941 (t)
REVERT: D  465 ASN cc_start: 0.8617 (p0) cc_final: 0.8307 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1822
  time to fit residues: 28.3406
Evaluate side-chains
  110 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN
D  35 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8469  Z= 0.324
  Angle     :  0.562   5.725  11869  Z= 0.287
  Chirality :  0.039   0.184   1384
  Planarity :  0.004   0.049   1229
  Dihedral  : 17.797 116.562   2040
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.06 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.31), residues: 805
  helix:  0.89 (0.31), residues: 272
  sheet: -1.64 (0.45), residues: 146
  loop : -0.40 (0.35), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 354 
 HIS   0.003   0.001   HIS A 211 
 PHE   0.011   0.002   PHE A 244 
 TYR   0.015   0.002   TYR D 155 
 ARG   0.004   0.001   ARG A 214 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7247 (mtp180)
REVERT: A  205 GLN cc_start: 0.6775 (tm-30) cc_final: 0.6181 (tm-30)
REVERT: B   40 MET cc_start: 0.6452 (mtp) cc_final: 0.6009 (mtp)
REVERT: B   59 GLN cc_start: 0.8416 (mp10) cc_final: 0.7946 (mp10)
REVERT: B   65 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8068 (tt)
REVERT: B  124 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8448 (mmtp)
REVERT: B  161 LEU cc_start: 0.8233 (mt) cc_final: 0.7867 (pt)
REVERT: C   44 MET cc_start: 0.7874 (tpp) cc_final: 0.7664 (tpt)
REVERT: C   47 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.7000 (p0)
REVERT: C  348 TYR cc_start: 0.7943 (t80) cc_final: 0.7356 (t80)
REVERT: D   63 TRP cc_start: 0.8629 (m100) cc_final: 0.8411 (m100)
REVERT: D   90 GLU cc_start: 0.8467 (tt0) cc_final: 0.8174 (pm20)
REVERT: D  460 THR cc_start: 0.9255 (p) cc_final: 0.8919 (t)
REVERT: D  465 ASN cc_start: 0.8633 (p0) cc_final: 0.8272 (p0)
REVERT: D  478 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8659 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1888
  time to fit residues: 30.1317
Evaluate side-chains
  117 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue   47 ASN
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  478 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 28 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8469  Z= 0.171
  Angle     :  0.495   5.787  11869  Z= 0.252
  Chirality :  0.036   0.186   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 17.744 114.352   2040
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.54 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.32), residues: 805
  helix:  1.18 (0.32), residues: 272
  sheet: -1.12 (0.47), residues: 134
  loop : -0.37 (0.35), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 354 
 HIS   0.002   0.001   HIS A 211 
 PHE   0.011   0.001   PHE A 233 
 TYR   0.014   0.001   TYR D 470 
 ARG   0.004   0.000   ARG A 193 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7652 (mmt-90) cc_final: 0.7180 (mtp180)
REVERT: A  205 GLN cc_start: 0.6801 (tm-30) cc_final: 0.6228 (tm-30)
REVERT: B   40 MET cc_start: 0.6265 (mtp) cc_final: 0.5881 (mtp)
REVERT: B   59 GLN cc_start: 0.8291 (mp10) cc_final: 0.7783 (mp10)
REVERT: B   88 GLN cc_start: 0.8744 (pp30) cc_final: 0.8504 (pp30)
REVERT: B  124 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8456 (mmtp)
REVERT: B  161 LEU cc_start: 0.8214 (mt) cc_final: 0.7855 (pt)
REVERT: C   44 MET cc_start: 0.7843 (tpp) cc_final: 0.7560 (tpt)
REVERT: C   47 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6774 (p0)
REVERT: C  348 TYR cc_start: 0.7785 (t80) cc_final: 0.7280 (t80)
REVERT: D   63 TRP cc_start: 0.8588 (m100) cc_final: 0.8331 (m100)
REVERT: D   90 GLU cc_start: 0.8380 (tt0) cc_final: 0.8073 (pm20)
REVERT: D  460 THR cc_start: 0.9181 (p) cc_final: 0.8876 (t)
REVERT: D  465 ASN cc_start: 0.8603 (p0) cc_final: 0.8234 (p0)
  outliers start: 15
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1910
  time to fit residues: 28.1167
Evaluate side-chains
  110 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain B residue   49 MET
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue   47 ASN
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  479 ASP
Chi-restraints excluded: chain D residue  519 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    0.1980
   chunk 48 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 85 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0770
   overall best weight:    1.2544

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8469  Z= 0.264
  Angle     :  0.528   5.774  11869  Z= 0.268
  Chirality :  0.038   0.183   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 17.732 113.902   2040
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.40 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.31), residues: 805
  helix:  1.07 (0.32), residues: 274
  sheet: -1.14 (0.47), residues: 134
  loop : -0.43 (0.35), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 354 
 HIS   0.002   0.001   HIS A 211 
 PHE   0.014   0.002   PHE A 233 
 TYR   0.013   0.002   TYR D 155 
 ARG   0.004   0.000   ARG A 193 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.7189 (mtp180)
REVERT: A  205 GLN cc_start: 0.6813 (tm-30) cc_final: 0.6190 (tm-30)
REVERT: B   40 MET cc_start: 0.6331 (mtp) cc_final: 0.5874 (mtp)
REVERT: B   59 GLN cc_start: 0.8334 (mp10) cc_final: 0.7823 (mp10)
REVERT: B   65 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8058 (tt)
REVERT: B  124 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8466 (mmtp)
REVERT: B  161 LEU cc_start: 0.8200 (mt) cc_final: 0.7836 (pt)
REVERT: C  348 TYR cc_start: 0.7882 (t80) cc_final: 0.7375 (t80)
REVERT: D   63 TRP cc_start: 0.8608 (m100) cc_final: 0.8347 (m100)
REVERT: D   90 GLU cc_start: 0.8417 (tt0) cc_final: 0.8036 (pm20)
REVERT: D  460 THR cc_start: 0.9201 (p) cc_final: 0.8890 (t)
REVERT: D  465 ASN cc_start: 0.8632 (p0) cc_final: 0.8245 (p0)
REVERT: D  478 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8629 (t80)
  outliers start: 18
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1856
  time to fit residues: 28.9172
Evaluate side-chains
  109 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  478 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    0.0270
   chunk 54 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8469  Z= 0.180
  Angle     :  0.495   5.858  11869  Z= 0.252
  Chirality :  0.037   0.185   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 17.695 112.369   2040
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.54 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.31), residues: 805
  helix:  1.27 (0.32), residues: 274
  sheet: -1.03 (0.46), residues: 134
  loop : -0.38 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 354 
 HIS   0.002   0.001   HIS A 211 
 PHE   0.012   0.001   PHE A 233 
 TYR   0.016   0.001   TYR D 470 
 ARG   0.005   0.000   ARG A 193 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7204 (mtp180)
REVERT: A  205 GLN cc_start: 0.6788 (tm-30) cc_final: 0.6221 (tm-30)
REVERT: B   40 MET cc_start: 0.6255 (mtp) cc_final: 0.5797 (mtp)
REVERT: B   59 GLN cc_start: 0.8332 (mp10) cc_final: 0.7824 (mp10)
REVERT: B   65 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8033 (tt)
REVERT: B  124 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8467 (mmtp)
REVERT: B  152 TYR cc_start: 0.8189 (m-80) cc_final: 0.7943 (m-80)
REVERT: B  161 LEU cc_start: 0.8166 (mt) cc_final: 0.7797 (pt)
REVERT: C  348 TYR cc_start: 0.7814 (t80) cc_final: 0.7323 (t80)
REVERT: D   63 TRP cc_start: 0.8591 (m100) cc_final: 0.8281 (m100)
REVERT: D   90 GLU cc_start: 0.8371 (tt0) cc_final: 0.8071 (pm20)
REVERT: D  460 THR cc_start: 0.9155 (p) cc_final: 0.8869 (t)
REVERT: D  465 ASN cc_start: 0.8618 (p0) cc_final: 0.8226 (p0)
  outliers start: 18
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1887
  time to fit residues: 29.7622
Evaluate side-chains
  114 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue   68 LYS
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  479 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 72 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0170
   chunk 79 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0070
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8469  Z= 0.179
  Angle     :  0.499   7.421  11869  Z= 0.254
  Chirality :  0.036   0.180   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 17.644 110.830   2040
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.98 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.31), residues: 805
  helix:  1.34 (0.32), residues: 274
  sheet: -0.96 (0.46), residues: 134
  loop : -0.38 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 354 
 HIS   0.002   0.001   HIS A 217 
 PHE   0.010   0.001   PHE A 233 
 TYR   0.014   0.001   TYR D 470 
 ARG   0.005   0.000   ARG A 193 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7634 (mmt-90) cc_final: 0.7217 (mtp180)
REVERT: A  205 GLN cc_start: 0.6770 (tm-30) cc_final: 0.6192 (tm-30)
REVERT: B   40 MET cc_start: 0.6282 (mtp) cc_final: 0.5806 (mtp)
REVERT: B   59 GLN cc_start: 0.8331 (mp10) cc_final: 0.7828 (mp10)
REVERT: B   65 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8004 (tt)
REVERT: B  124 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8469 (mmtp)
REVERT: B  152 TYR cc_start: 0.8169 (m-80) cc_final: 0.7541 (m-80)
REVERT: B  161 LEU cc_start: 0.8145 (mt) cc_final: 0.7775 (pt)
REVERT: C  348 TYR cc_start: 0.7656 (t80) cc_final: 0.7231 (t80)
REVERT: C  354 TRP cc_start: 0.7296 (m100) cc_final: 0.6493 (m100)
REVERT: D   63 TRP cc_start: 0.8590 (m100) cc_final: 0.8262 (m100)
REVERT: D   90 GLU cc_start: 0.8362 (tt0) cc_final: 0.8080 (pm20)
REVERT: D  460 THR cc_start: 0.9150 (p) cc_final: 0.8869 (t)
REVERT: D  465 ASN cc_start: 0.8624 (p0) cc_final: 0.8234 (p0)
REVERT: D  478 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8647 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 109
  average time/residue: 0.2055
  time to fit residues: 30.9129
Evaluate side-chains
  109 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  479 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0980
   chunk 21 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 GLN
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8469  Z= 0.247
  Angle     :  0.530   7.107  11869  Z= 0.269
  Chirality :  0.037   0.181   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 17.657 110.586   2040
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.69 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.31), residues: 805
  helix:  1.21 (0.31), residues: 275
  sheet: -0.98 (0.46), residues: 134
  loop : -0.38 (0.35), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 354 
 HIS   0.002   0.001   HIS A 211 
 PHE   0.016   0.001   PHE A 233 
 TYR   0.014   0.001   TYR D 470 
 ARG   0.005   0.000   ARG A 193 

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7188 (mtp180)
REVERT: B   40 MET cc_start: 0.6400 (mtp) cc_final: 0.5934 (mtp)
REVERT: B   59 GLN cc_start: 0.8353 (mp10) cc_final: 0.7808 (mp10)
REVERT: B   65 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8004 (tt)
REVERT: B  124 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8474 (mmtp)
REVERT: B  161 LEU cc_start: 0.8213 (mt) cc_final: 0.7851 (pt)
REVERT: C  348 TYR cc_start: 0.7712 (t80) cc_final: 0.7265 (t80)
REVERT: C  354 TRP cc_start: 0.7378 (m100) cc_final: 0.6580 (m100)
REVERT: D   63 TRP cc_start: 0.8597 (m100) cc_final: 0.8298 (m100)
REVERT: D   90 GLU cc_start: 0.8405 (tt0) cc_final: 0.8090 (pm20)
REVERT: D  460 THR cc_start: 0.9167 (p) cc_final: 0.8877 (t)
REVERT: D  465 ASN cc_start: 0.8652 (p0) cc_final: 0.8255 (p0)
REVERT: D  478 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8611 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 104
  average time/residue: 0.2028
  time to fit residues: 29.1492
Evaluate side-chains
  105 residues out of total 698 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  479 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 70 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 13 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.158089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.119394 restraints weight = 12352.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.40
r_work: 0.3458 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   8469  Z= 0.172
  Angle     :  0.525   8.652  11869  Z= 0.270
  Chirality :  0.037   0.180   1384
  Planarity :  0.005   0.071   1229
  Dihedral  : 17.675 110.292   2040
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.28 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.31), residues: 805
  helix:  1.30 (0.32), residues: 274
  sheet: -0.90 (0.47), residues: 134
  loop : -0.40 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 354 
 HIS   0.002   0.001   HIS A 217 
 PHE   0.017   0.001   PHE C 305 
 TYR   0.014   0.001   TYR D 470 
 ARG   0.009   0.000   ARG C 340 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1914.39 seconds
wall clock time: 35 minutes 14.38 seconds (2114.38 seconds total)