Starting phenix.real_space_refine
on Tue Mar  3 20:25:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wb1_21584/03_2026/6wb1_21584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wb1_21584/03_2026/6wb1_21584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2026/6wb1_21584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2026/6wb1_21584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2026/6wb1_21584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wb1_21584/03_2026/6wb1_21584.cif"
  }
  resolution = 4.7
  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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P      72      5.49       5
     S       5      5.16       5
     C    5029      2.51       5
     N    1444      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8235
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 705
          Classifications: {'RNA': 33}
          Modifications used: {'5*END': 1, 'rna3p_pur': 19, 'rna3p_pyr': 13}
          Link IDs: {'rna3p': 32}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 880
          Inner-chain residues flagged as termini: ['pdbres="  G D  46 "']
          Classifications: {'DNA': 4, 'RNA': 38}
          Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21}
          Link IDs: {'rna3p': 41}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 3716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 3716
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 196}
          Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 507}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 716
          Unresolved non-hydrogen angles: 883
          Unresolved non-hydrogen dihedrals: 575
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'GLU:plan': 40, 'GLN:plan1': 20, 'ASN:plan1': 6, 'PHE:plan': 5, 'ASP:plan': 16, 'TRP:plan': 1, 'ARG:plan': 6, 'HIS:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 397
    Chain: "B"
      Number of atoms: 2934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2934
          Classifications: {'peptide': 402}
          Incomplete info: {'truncation_to_alanine': 107}
          Link IDs: {'PTRANS': 30, 'TRANS': 371}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 396
          Unresolved non-hydrogen angles: 488
          Unresolved non-hydrogen dihedrals: 323
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLU:plan': 27, 'ASP:plan': 11, 'TRP:plan': 1, 'GLN:plan1': 10, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 228
  Time building chain proxies: 1.95, per 1000 atoms: 0.24
  Number of scatterers: 8235
  At special positions: 0
  Unit cell: (99.64, 97.52, 119.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       5     16.00
     P      72     15.00
     O    1685      8.00
     N    1444      7.00
     C    5029      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: 0.83
  Conformation dependent library (CDL) restraints added in 229.5 milliseconds
  

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1782

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      39.2% alpha, 7.0% beta
      38 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 44
      removed outlier: 3.706A  pdb=" N   ALA A  33 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.611A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.745A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 211
      removed outlier: 3.558A  pdb=" N   HIS A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 269
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 363 through 383
      removed outlier: 3.624A  pdb=" N   GLN A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
      removed outlier: 3.693A  pdb=" N   TRP A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.600A  pdb=" N   ASP A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 3.542A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
      removed outlier: 3.591A  pdb=" N   ASN A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LYS A 527 " --> pdb=" O   GLU A 523 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LYS A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'B' and resid 27 through 44
      removed outlier: 4.051A  pdb=" N   ALA B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLU B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 91
      removed outlier: 6.232A  pdb=" N   ASP B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   PHE B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 103
      removed outlier: 3.751A  pdb=" N   LYS B 101 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.810A  pdb=" N   ALA B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 154 through 175
      removed outlier: 3.553A  pdb=" N   ALA B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.772A  pdb=" N   LYS B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLN B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 211
    Processing helix  chain 'B' and resid 253 through 268
    Processing helix  chain 'B' and resid 276 through 284
      removed outlier: 3.509A  pdb=" N   LYS B 281 " --> pdb=" O   ARG B 277 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 312
      removed outlier: 3.725A  pdb=" N   GLU B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 384
      removed outlier: 3.738A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.839A  pdb=" N   TRP B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 427
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107
      removed outlier: 3.893A  pdb=" N   GLY A 190 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL A 179 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 351
      removed outlier: 6.884A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ALA A 327 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362
      removed outlier: 3.714A  pdb=" N   LYS A 512 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441
      removed outlier: 6.283A  pdb=" N   PHE A 440 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 443 through 444
      removed outlier: 4.028A  pdb=" N   ASP A 443 " --> pdb=" O   GLY A 456 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLY A 456 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49
      removed outlier: 3.792A  pdb=" N   ILE B 142 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE B 132 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE B 130 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 107
    Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 181
      removed outlier: 3.847A  pdb=" N   TYR B 181 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 350
      removed outlier: 7.107A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   THR B 338 " --> pdb=" O   GLN B 330 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN B 330 " --> pdb=" O   THR B 338 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE B 329 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    711 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      99 hydrogen bonds
      186 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2221
        1.34 -     1.45: 1911
        1.45 -     1.57: 4322
        1.57 -     1.69: 143
        1.69 -     1.81: 8
  Bond restraints: 8605
  Sorted by residual:
  bond pdb=" C5   DC D  77 "
       pdb=" C6   DC D  77 "
    ideal  model  delta    sigma   weight residual
    1.337  1.360 -0.023 2.00e-02 2.50e+03 1.37e+00
  bond pdb=" CG  PRO A 226 "
       pdb=" CD  PRO A 226 "
    ideal  model  delta    sigma   weight residual
    1.512  1.483  0.029 2.70e-02 1.37e+03 1.14e+00
  bond pdb=" CA  GLN B 332 "
       pdb=" C   GLN B 332 "
    ideal  model  delta    sigma   weight residual
    1.519  1.530 -0.011 1.01e-02 9.80e+03 1.09e+00
  bond pdb=" C   LEU B 149 "
       pdb=" N   PRO B 150 "
    ideal  model  delta    sigma   weight residual
    1.326  1.341 -0.015 1.44e-02 4.82e+03 1.08e+00
  bond pdb=" C   LEU A 149 "
       pdb=" N   PRO A 150 "
    ideal  model  delta    sigma   weight residual
    1.326  1.340 -0.014 1.44e-02 4.82e+03 9.61e-01
  ... (remaining 8600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 11952
        1.47 -     2.95: 155
        2.95 -     4.42: 60
        4.42 -     5.89: 2
        5.89 -     7.36: 1
  Bond angle restraints: 12170
  Sorted by residual:
  angle pdb=" N   VAL A 276 "
        pdb=" CA  VAL A 276 "
        pdb=" C   VAL A 276 "
      ideal   model   delta    sigma   weight residual
     113.20  109.76    3.44 9.60e-01 1.09e+00 1.29e+01
  angle pdb=" CA  LYS B  13 "
        pdb=" C   LYS B  13 "
        pdb=" N   PRO B  14 "
      ideal   model   delta    sigma   weight residual
     118.83  116.42    2.41 8.70e-01 1.32e+00 7.69e+00
  angle pdb=" N   TYR A 115 "
        pdb=" CA  TYR A 115 "
        pdb=" C   TYR A 115 "
      ideal   model   delta    sigma   weight residual
     111.07  108.19    2.88 1.07e+00 8.73e-01 7.24e+00
  angle pdb=" C2'   C C 134 "
        pdb=" C1'   C C 134 "
        pdb=" N1    C C 134 "
      ideal   model   delta    sigma   weight residual
     112.40  119.76   -7.36 3.00e+00 1.11e-01 6.02e+00
  angle pdb=" N   ARG A 307 "
        pdb=" CA  ARG A 307 "
        pdb=" C   ARG A 307 "
      ideal   model   delta    sigma   weight residual
     111.07  108.64    2.43 1.07e+00 8.73e-01 5.17e+00
  ... (remaining 12165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4602
       17.79 -    35.58: 289
       35.58 -    53.37: 120
       53.37 -    71.16: 87
       71.16 -    88.95: 27
  Dihedral angle restraints: 5125
    sinusoidal: 2372
      harmonic: 2753
  Sorted by residual:
  dihedral pdb=" N   GLU B 378 "
           pdb=" CA  GLU B 378 "
           pdb=" CB  GLU B 378 "
           pdb=" CG  GLU B 378 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.88   54.88     3      1.50e+01 4.44e-03 9.31e+00
  dihedral pdb=" O5'   U C 135 "
           pdb=" C5'   U C 135 "
           pdb=" C4'   U C 135 "
           pdb=" C3'   U C 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.00  122.72   52.28     3      1.50e+01 4.44e-03 9.10e+00
  dihedral pdb=" N   GLU B  79 "
           pdb=" CA  GLU B  79 "
           pdb=" CB  GLU B  79 "
           pdb=" CG  GLU B  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.51   50.51     3      1.50e+01 4.44e-03 8.91e+00
  ... (remaining 5122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1226
       0.045 -    0.091: 158
       0.091 -    0.136: 74
       0.136 -    0.181: 2
       0.181 -    0.227: 3
  Chirality restraints: 1463
  Sorted by residual:
  chirality pdb=" C1'   C C 134 "
            pdb=" O4'   C C 134 "
            pdb=" C2'   C C 134 "
            pdb=" N1    C C 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.23    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C3'  DT D  78 "
            pdb=" C4'  DT D  78 "
            pdb=" O3'  DT D  78 "
            pdb=" C2'  DT D  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.47   -0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" C3'  DG D  73 "
            pdb=" C4'  DG D  73 "
            pdb=" O3'  DG D  73 "
            pdb=" C2'  DG D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.48   -0.18 2.00e-01 2.50e+01 8.32e-01
  ... (remaining 1460 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 224 "    0.037 5.00e-02 4.00e+02   5.54e-02 4.91e+00
        pdb=" N   PRO A 225 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 225 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 225 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 257 "   -0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   ILE A 257 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE A 257 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 258 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D  78 "    0.010 2.00e-02 2.50e+03   7.34e-03 1.35e+00
        pdb=" N1   DT D  78 "    0.009 2.00e-02 2.50e+03
        pdb=" C2   DT D  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DT D  78 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3   DT D  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DT D  78 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT D  78 "    0.012 2.00e-02 2.50e+03
        pdb=" C5   DT D  78 "   -0.005 2.00e-02 2.50e+03
        pdb=" C7   DT D  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT D  78 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 984
        2.74 -     3.28: 8367
        3.28 -     3.82: 14066
        3.82 -     4.36: 15575
        4.36 -     4.90: 24636
  Nonbonded interactions: 63628
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 321 "
            pdb=" NZ  LYS B 385 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ARG A 211 "
            pdb=" NE  ARG A 211 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OG  SER A 105 "
            pdb=" OG  SER A 191 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ALA A 538 "
            pdb=" NZ  LYS A 540 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   TRP A 239 "
            pdb=" N   GLY A 316 "
     model   vdw
     2.302 3.120
  ... (remaining 63623 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.400
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.330
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
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      :  0.002   0.029   8605  Z= 0.112
  Angle     :  0.500   7.364  12170  Z= 0.273
  Chirality :  0.039   0.227   1463
  Planarity :  0.003   0.055   1272
  Dihedral  : 17.215  88.947   3343
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.54 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  1.28 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.82 (0.23), residues: 926
  helix: -1.78 (0.24), residues: 325
  sheet: -4.65 (0.28), residues: 147
  loop : -3.82 (0.24), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 199 
 TYR   0.010   0.001   TYR B 354 
 PHE   0.006   0.001   PHE A 227 
 TRP   0.012   0.001   TRP A 402 
 HIS   0.003   0.000   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 8605)
  covalent geometry    : angle       0.50046 (12170)
  hydrogen bonds       : bond        0.16206 (  359)
  hydrogen bonds       : angle       5.71107 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 LYS cc_start: 0.9720 (tppp) cc_final: 0.9464 (mptt)
REVERT: B   42 GLU cc_start: 0.9454 (tt0) cc_final: 0.9173 (tt0)
REVERT: B  206 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8940 (ttm170)
REVERT: B  307 ARG cc_start: 0.9207 (mtm180) cc_final: 0.8985 (mtt-85)
REVERT: B  320 ASP cc_start: 0.8915 (t0) cc_final: 0.8595 (t70)
REVERT: B  378 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9192 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1242
  time to fit residues: 16.4953
Evaluate side-chains
  54 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.4980
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0670
   overall best weight:    1.8520

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

Flipped N/Q/H residues before XYZ refinement:
A 306 ASN
A 475 GLN
B  57 ASN
B 147 ASN
B 161 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.058432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.047170 restraints weight = 64382.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.048217 restraints weight = 40770.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.048983 restraints weight = 28832.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.049517 restraints weight = 21901.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.049933 restraints weight = 17734.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8605  Z= 0.150
  Angle     :  0.569   8.104  12170  Z= 0.283
  Chirality :  0.039   0.144   1463
  Planarity :  0.004   0.065   1272
  Dihedral  : 18.499  91.000   2135
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.92 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.26), residues: 926
  helix: -0.31 (0.28), residues: 342
  sheet: -3.58 (0.36), residues: 130
  loop : -3.25 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 211 
 TYR   0.014   0.002   TYR A 501 
 PHE   0.013   0.002   PHE B 416 
 TRP   0.018   0.002   TRP B 410 
 HIS   0.004   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8605)
  covalent geometry    : angle       0.56939 (12170)
  hydrogen bonds       : bond        0.05842 (  359)
  hydrogen bonds       : angle       4.16262 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9062 (ttm110) cc_final: 0.8606 (tpt90)
REVERT: B  115 TYR cc_start: 0.8457 (m-80) cc_final: 0.8026 (m-80)
REVERT: B  183 TYR cc_start: 0.8251 (t80) cc_final: 0.7993 (t80)
REVERT: B  184 MET cc_start: 0.7837 (mmp) cc_final: 0.7509 (mmp)
REVERT: B  206 ARG cc_start: 0.9255 (mtp180) cc_final: 0.9046 (ttm170)
REVERT: B  320 ASP cc_start: 0.8886 (t0) cc_final: 0.8600 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0824
  time to fit residues: 7.8563
Evaluate side-chains
  49 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 545 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.042580 restraints weight = 60504.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.043629 restraints weight = 37526.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.044373 restraints weight = 26023.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.044908 restraints weight = 19676.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.045286 restraints weight = 15826.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8605  Z= 0.180
  Angle     :  0.582  12.031  12170  Z= 0.288
  Chirality :  0.039   0.163   1463
  Planarity :  0.004   0.058   1272
  Dihedral  : 18.731  92.371   2135
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.75 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.27), residues: 926
  helix:  0.36 (0.29), residues: 341
  sheet: -3.00 (0.37), residues: 134
  loop : -2.75 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 463 
 TYR   0.013   0.002   TYR A 127 
 PHE   0.023   0.002   PHE B 416 
 TRP   0.019   0.002   TRP B 410 
 HIS   0.004   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8605)
  covalent geometry    : angle       0.58232 (12170)
  hydrogen bonds       : bond        0.05938 (  359)
  hydrogen bonds       : angle       4.04544 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8717 (tpt90)
REVERT: B   41 MET cc_start: 0.8572 (mtm) cc_final: 0.8298 (mtt)
REVERT: B   42 GLU cc_start: 0.9478 (tt0) cc_final: 0.9173 (tp30)
REVERT: B  320 ASP cc_start: 0.8781 (t0) cc_final: 0.8399 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0887
  time to fit residues: 6.6897
Evaluate side-chains
  46 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.055611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.044205 restraints weight = 65812.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.045198 restraints weight = 41316.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.045918 restraints weight = 29093.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.046454 restraints weight = 22152.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.046789 restraints weight = 17917.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8605  Z= 0.111
  Angle     :  0.518   7.906  12170  Z= 0.248
  Chirality :  0.037   0.135   1463
  Planarity :  0.004   0.063   1272
  Dihedral  : 18.458  84.859   2135
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.28), residues: 926
  helix:  0.72 (0.30), residues: 345
  sheet: -2.33 (0.41), residues: 130
  loop : -2.32 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 143 
 TYR   0.009   0.001   TYR A 501 
 PHE   0.009   0.001   PHE A 227 
 TRP   0.018   0.001   TRP A 402 
 HIS   0.002   0.001   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8605)
  covalent geometry    : angle       0.51825 (12170)
  hydrogen bonds       : bond        0.04730 (  359)
  hydrogen bonds       : angle       3.74960 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8639 (tpt90)
REVERT: B   41 MET cc_start: 0.8572 (mtm) cc_final: 0.8151 (mtt)
REVERT: B   42 GLU cc_start: 0.9327 (tt0) cc_final: 0.8898 (tp30)
REVERT: B  145 GLN cc_start: 0.8481 (tt0) cc_final: 0.8180 (tm-30)
REVERT: B  183 TYR cc_start: 0.8446 (t80) cc_final: 0.8068 (t80)
REVERT: B  184 MET cc_start: 0.8024 (mmp) cc_final: 0.7761 (mmp)
REVERT: B  320 ASP cc_start: 0.8795 (t0) cc_final: 0.8570 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0806
  time to fit residues: 6.3327
Evaluate side-chains
  44 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0070
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    0.1980
   chunk 97 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
A 447 ASN
B 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.055704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.043779 restraints weight = 58910.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.044877 restraints weight = 35919.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.045547 restraints weight = 24754.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.046175 restraints weight = 19212.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.046571 restraints weight = 15202.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8605  Z= 0.088
  Angle     :  0.496   8.116  12170  Z= 0.234
  Chirality :  0.037   0.141   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.283  80.571   2135
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.29), residues: 926
  helix:  0.99 (0.30), residues: 347
  sheet: -1.85 (0.44), residues: 131
  loop : -2.04 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 125 
 TYR   0.008   0.001   TYR A 501 
 PHE   0.010   0.001   PHE B 130 
 TRP   0.033   0.001   TRP B 398 
 HIS   0.002   0.000   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 8605)
  covalent geometry    : angle       0.49648 (12170)
  hydrogen bonds       : bond        0.04214 (  359)
  hydrogen bonds       : angle       3.61233 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8595 (tpt90)
REVERT: B   41 MET cc_start: 0.8600 (mtm) cc_final: 0.8174 (mtt)
REVERT: B   42 GLU cc_start: 0.9400 (tt0) cc_final: 0.8849 (tp30)
REVERT: B  145 GLN cc_start: 0.8636 (tt0) cc_final: 0.8310 (tm-30)
REVERT: B  320 ASP cc_start: 0.8838 (t0) cc_final: 0.8561 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0767
  time to fit residues: 6.5764
Evaluate side-chains
  43 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 85 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 93 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.053374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.042189 restraints weight = 65534.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.043199 restraints weight = 40441.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.043905 restraints weight = 28104.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.044395 restraints weight = 21341.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.044771 restraints weight = 17343.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8605  Z= 0.154
  Angle     :  0.545  10.461  12170  Z= 0.262
  Chirality :  0.037   0.140   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.550  85.920   2135
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.28), residues: 926
  helix:  0.89 (0.30), residues: 353
  sheet: -1.80 (0.43), residues: 128
  loop : -2.12 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.020   0.002   TYR B 146 
 PHE   0.012   0.002   PHE A 227 
 TRP   0.012   0.002   TRP A 402 
 HIS   0.004   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8605)
  covalent geometry    : angle       0.54486 (12170)
  hydrogen bonds       : bond        0.05244 (  359)
  hydrogen bonds       : angle       3.78129 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8537 (mtm) cc_final: 0.8161 (mtt)
REVERT: B  183 TYR cc_start: 0.8669 (t80) cc_final: 0.8425 (t80)
REVERT: B  320 ASP cc_start: 0.8765 (t0) cc_final: 0.8433 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0681
  time to fit residues: 4.9995
Evaluate side-chains
  42 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 69 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.053606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.042438 restraints weight = 66347.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.043409 restraints weight = 41633.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.044092 restraints weight = 29337.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.044563 restraints weight = 22473.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.044932 restraints weight = 18401.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8605  Z= 0.129
  Angle     :  0.529   9.556  12170  Z= 0.253
  Chirality :  0.037   0.144   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.498  83.653   2135
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.29), residues: 926
  helix:  0.97 (0.30), residues: 354
  sheet: -1.56 (0.43), residues: 135
  loop : -1.95 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 463 
 TYR   0.010   0.001   TYR B 146 
 PHE   0.011   0.001   PHE A 227 
 TRP   0.012   0.001   TRP A 402 
 HIS   0.003   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8605)
  covalent geometry    : angle       0.52884 (12170)
  hydrogen bonds       : bond        0.04847 (  359)
  hydrogen bonds       : angle       3.90370 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8599 (mtm) cc_final: 0.8260 (mtt)
REVERT: B   42 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8699 (tp30)
REVERT: B  145 GLN cc_start: 0.8669 (tt0) cc_final: 0.8163 (tm-30)
REVERT: B  320 ASP cc_start: 0.8818 (t0) cc_final: 0.8494 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0670
  time to fit residues: 5.0266
Evaluate side-chains
  40 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 79 optimal weight:    0.5980
   chunk 4 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.054498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.043208 restraints weight = 64638.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.044233 restraints weight = 39557.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.044977 restraints weight = 27413.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.045472 restraints weight = 20641.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.045859 restraints weight = 16721.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8605  Z= 0.094
  Angle     :  0.505   8.144  12170  Z= 0.238
  Chirality :  0.036   0.143   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.328  81.789   2135
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.29), residues: 926
  helix:  1.34 (0.30), residues: 342
  sheet: -1.34 (0.42), residues: 146
  loop : -1.72 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.008   0.001   TYR A 501 
 PHE   0.009   0.001   PHE B 416 
 TRP   0.014   0.001   TRP A  88 
 HIS   0.001   0.000   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 8605)
  covalent geometry    : angle       0.50513 (12170)
  hydrogen bonds       : bond        0.04241 (  359)
  hydrogen bonds       : angle       3.77657 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8328 (mtm) cc_final: 0.8055 (mtt)
REVERT: B  145 GLN cc_start: 0.8356 (tt0) cc_final: 0.8009 (tm-30)
REVERT: B  184 MET cc_start: 0.8371 (mmp) cc_final: 0.8137 (mmp)
REVERT: B  320 ASP cc_start: 0.8848 (t0) cc_final: 0.8572 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0670
  time to fit residues: 5.1985
Evaluate side-chains
  41 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 18 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 99 optimal weight:    0.1980
   chunk 69 optimal weight:    0.0070
   chunk 46 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0270
   chunk 65 optimal weight:    0.0770
   overall best weight:    0.1614

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.055919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.044315 restraints weight = 63178.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.045366 restraints weight = 38237.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.046132 restraints weight = 26415.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.046663 restraints weight = 19933.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.047061 restraints weight = 16112.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8605  Z= 0.087
  Angle     :  0.503   8.220  12170  Z= 0.238
  Chirality :  0.037   0.142   1463
  Planarity :  0.004   0.060   1272
  Dihedral  : 18.162  79.796   2135
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.29), residues: 926
  helix:  1.43 (0.30), residues: 344
  sheet: -1.15 (0.41), residues: 156
  loop : -1.57 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.009   0.001   TYR B 144 
 PHE   0.008   0.001   PHE B 130 
 TRP   0.033   0.001   TRP A  88 
 HIS   0.002   0.000   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 8605)
  covalent geometry    : angle       0.50305 (12170)
  hydrogen bonds       : bond        0.03793 (  359)
  hydrogen bonds       : angle       3.69853 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 PHE cc_start: 0.8925 (t80) cc_final: 0.8653 (t80)
REVERT: B   41 MET cc_start: 0.8459 (mtm) cc_final: 0.8117 (mtt)
REVERT: B  115 TYR cc_start: 0.8752 (m-80) cc_final: 0.8150 (m-80)
REVERT: B  184 MET cc_start: 0.8450 (mmp) cc_final: 0.8092 (mmp)
REVERT: B  320 ASP cc_start: 0.8852 (t0) cc_final: 0.8614 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0685
  time to fit residues: 6.0818
Evaluate side-chains
  43 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0070
   chunk 4 optimal weight:   20.0000
   chunk 85 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.8002

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B 147 ASN
B 330 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.042647 restraints weight = 65394.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.043641 restraints weight = 40559.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.044330 restraints weight = 28383.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.044843 restraints weight = 21650.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.045183 restraints weight = 17570.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8605  Z= 0.131
  Angle     :  0.528  10.489  12170  Z= 0.252
  Chirality :  0.037   0.140   1463
  Planarity :  0.005   0.089   1272
  Dihedral  : 18.339  84.062   2135
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.29), residues: 926
  helix:  1.42 (0.30), residues: 349
  sheet: -1.14 (0.41), residues: 156
  loop : -1.66 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 143 
 TYR   0.010   0.001   TYR A 501 
 PHE   0.011   0.001   PHE A 227 
 TRP   0.015   0.001   TRP A  88 
 HIS   0.004   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8605)
  covalent geometry    : angle       0.52759 (12170)
  hydrogen bonds       : bond        0.04591 (  359)
  hydrogen bonds       : angle       3.82243 (  897)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: B   41 MET cc_start: 0.8532 (mtm) cc_final: 0.8181 (mtt)
REVERT: B  184 MET cc_start: 0.8570 (mmp) cc_final: 0.8340 (mmm)
REVERT: B  320 ASP cc_start: 0.8798 (t0) cc_final: 0.8511 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0643
  time to fit residues: 4.7057
Evaluate side-chains
  40 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 77 optimal weight:    0.2980
   chunk 33 optimal weight:    0.0030
   chunk 85 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.2394

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.054205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.042848 restraints weight = 65182.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.043866 restraints weight = 39682.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.044591 restraints weight = 27600.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.045118 restraints weight = 20983.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.045456 restraints weight = 16956.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8605  Z= 0.100
  Angle     :  0.512   8.742  12170  Z= 0.242
  Chirality :  0.037   0.174   1463
  Planarity :  0.004   0.066   1272
  Dihedral  : 18.301  82.630   2135
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.29), residues: 926
  helix:  1.41 (0.30), residues: 351
  sheet: -1.03 (0.41), residues: 156
  loop : -1.60 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 143 
 TYR   0.010   0.001   TYR B 146 
 PHE   0.016   0.001   PHE B 130 
 TRP   0.014   0.001   TRP A 402 
 HIS   0.002   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8605)
  covalent geometry    : angle       0.51194 (12170)
  hydrogen bonds       : bond        0.04280 (  359)
  hydrogen bonds       : angle       3.79166 (  897)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1158.28 seconds
wall clock time: 20 minutes 46.86 seconds (1246.86 seconds total)