Starting phenix.real_space_refine
on Thu Feb 13 08:26:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wb0_21583/02_2025/6wb0_21583.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wb0_21583/02_2025/6wb0_21583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wb0_21583/02_2025/6wb0_21583.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wb0_21583/02_2025/6wb0_21583.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wb0_21583/02_2025/6wb0_21583.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wb0_21583/02_2025/6wb0_21583.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      74      5.49       5
     S       6      5.16       5
     C    5186      2.51       5
     N    1481      2.21       5
     O    1771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8518
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 3911
          Classifications: {'peptide': 545}
          Incomplete info: {'truncation_to_alanine': 139}
          Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 510}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 546
          Unresolved non-hydrogen angles: 667
          Unresolved non-hydrogen dihedrals: 457
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 32, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 304
    Chain: "B"
      Number of atoms: 2979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 2979
          Classifications: {'peptide': 403}
          Incomplete info: {'truncation_to_alanine': 98}
          Link IDs: {'PTRANS': 30, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 356
          Unresolved non-hydrogen angles: 440
          Unresolved non-hydrogen dihedrals: 294
          Unresolved non-hydrogen chiralities: 31
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 168
    Chain: "C"
      Number of atoms: 747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 747
          Classifications: {'RNA': 35}
          Modifications used: {'5*END': 1, 'rna3p_pur': 20, 'rna3p_pyr': 14}
          Link IDs: {'rna3p': 34}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 881
          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: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 5.46, per 1000 atoms: 0.64
  Number of scatterers: 8518
  At special positions: 0
  Unit cell: (104.94, 107.06, 117.66, 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       6     16.00
     P      74     15.00
     O    1771      8.00
     N    1481      7.00
     C    5186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.51
  Conformation dependent library (CDL) restraints added in 876.9 milliseconds
  

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1786

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      39.6% alpha, 6.3% beta
      39 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 3.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 44
    Processing helix  chain 'A' and resid 77 through 84
      removed outlier: 4.292A  pdb=" N   LYS A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG A  83 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 114 through 118
      removed outlier: 3.779A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 4.256A  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: 3.579A  pdb=" N   HIS A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 363 through 383
    Processing helix  chain 'A' and resid 394 through 404
      removed outlier: 3.514A  pdb=" N   TRP A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.678A  pdb=" N   ASP A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 4.217A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 4.059A  pdb=" N   LYS A 527 " --> pdb=" O   GLU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 553
      removed outlier: 4.005A  pdb=" N   GLN A 547 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 44
      removed outlier: 4.139A  pdb=" N   ALA B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 91
      removed outlier: 6.165A  pdb=" N   ASP B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   PHE B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 103
    Processing helix  chain 'B' and resid 112 through 118
      removed outlier: 3.504A  pdb=" N   VAL B 118 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 4.140A  pdb=" N   LYS B 126 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.815A  pdb=" N   ASN B 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 175
      removed outlier: 5.158A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS B 166 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.883A  pdb=" N   GLN B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 212
      removed outlier: 4.461A  pdb=" N   TRP B 212 " --> pdb=" O   HIS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 269
      removed outlier: 3.944A  pdb=" N   GLN B 269 " --> pdb=" O   ASN B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 285
      removed outlier: 3.724A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   LEU B 282 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU B 283 " --> pdb=" O   SER B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 312
      removed outlier: 3.870A  pdb=" N   GLU B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 384
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.853A  pdb=" N   TRP B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 427
      removed outlier: 3.519A  pdb=" N   TYR B 427 " --> pdb=" O   LYS B 424 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108
      removed outlier: 3.866A  pdb=" N   GLY A 190 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   VAL A 179 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 234
    Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 329
      removed outlier: 7.304A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   THR A 351 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 391
    Processing sheet with id=AA5, first strand: chain 'A' and resid 439 through 441
      removed outlier: 6.524A  pdb=" N   PHE A 440 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 457
      removed outlier: 3.569A  pdb=" N   LYS A 465 " --> pdb=" O   TYR A 457 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 62
      removed outlier: 4.539A  pdb=" N   PHE B  61 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B  74 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110
    Processing sheet with id=AA9, first strand: chain 'B' and resid 129 through 131
      removed outlier: 4.050A  pdb=" N   PHE B 130 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253
      removed outlier: 4.479A  pdb=" N   TRP B 252 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ILE B 293 " --> pdb=" O   TRP B 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 339
      removed outlier: 3.858A  pdb=" N   THR B 338 " --> pdb=" O   GLN B 330 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLN B 330 " --> pdb=" O   THR B 338 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS B 390 " --> pdb=" O   ALA B 327 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE B 329 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    687 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      101 hydrogen bonds
      190 hydrogen bond angles
      0 basepair planarities
      39 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 3.16

  Time building geometry restraints manager: 2.81 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: 2420
        1.34 -     1.45: 1856
        1.45 -     1.57: 4461
        1.57 -     1.69: 147
        1.69 -     1.81: 9
  Bond restraints: 8893
  Sorted by residual:
  bond pdb=" N   PRO A  25 "
       pdb=" CD  PRO A  25 "
    ideal  model  delta    sigma   weight residual
    1.473  1.530 -0.057 1.40e-02 5.10e+03 1.65e+01
  bond pdb=" C5   DC D  77 "
       pdb=" C6   DC D  77 "
    ideal  model  delta    sigma   weight residual
    1.337  1.361 -0.024 2.00e-02 2.50e+03 1.41e+00
  bond pdb=" C   THR A 216 "
       pdb=" N   PRO A 217 "
    ideal  model  delta    sigma   weight residual
    1.326  1.341 -0.015 1.44e-02 4.82e+03 1.08e+00
  bond pdb=" C   GLU A 169 "
       pdb=" O   GLU A 169 "
    ideal  model  delta    sigma   weight residual
    1.241  1.231  0.010 9.80e-03 1.04e+04 1.07e+00
  bond pdb=" CG  PRO A 226 "
       pdb=" CD  PRO A 226 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.70e-02 1.37e+03 1.03e+00
  ... (remaining 8888 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 12220
        1.31 -     2.62: 240
        2.62 -     3.93: 82
        3.93 -     5.24: 4
        5.24 -     6.55: 3
  Bond angle restraints: 12549
  Sorted by residual:
  angle pdb=" CA  PRO A  25 "
        pdb=" N   PRO A  25 "
        pdb=" CD  PRO A  25 "
      ideal   model   delta    sigma   weight residual
     112.00  106.61    5.39 1.40e+00 5.10e-01 1.48e+01
  angle pdb=" CA  VAL A 467 "
        pdb=" C   VAL A 467 "
        pdb=" N   PRO A 468 "
      ideal   model   delta    sigma   weight residual
     116.57  119.44   -2.87 9.80e-01 1.04e+00 8.61e+00
  angle pdb=" N   ILE B 180 "
        pdb=" CA  ILE B 180 "
        pdb=" C   ILE B 180 "
      ideal   model   delta    sigma   weight residual
     108.48  112.47   -3.99 1.44e+00 4.82e-01 7.66e+00
  angle pdb=" CA  GLU A 169 "
        pdb=" C   GLU A 169 "
        pdb=" N   PRO A 170 "
      ideal   model   delta    sigma   weight residual
     120.79  118.14    2.65 9.70e-01 1.06e+00 7.44e+00
  angle pdb=" N   LYS A  49 "
        pdb=" CA  LYS A  49 "
        pdb=" C   LYS A  49 "
      ideal   model   delta    sigma   weight residual
     107.32  111.61   -4.29 1.65e+00 3.67e-01 6.75e+00
  ... (remaining 12544 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 4820
       17.60 -    35.21: 292
       35.21 -    52.81: 116
       52.81 -    70.42: 78
       70.42 -    88.02: 27
  Dihedral angle restraints: 5333
    sinusoidal: 2572
      harmonic: 2761
  Sorted by residual:
  dihedral pdb=" O5'   A D  50 "
           pdb=" C5'   A D  50 "
           pdb=" C4'   A D  50 "
           pdb=" C3'   A D  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -65.00   -7.52  -57.48     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CA  LYS B  73 "
           pdb=" CB  LYS B  73 "
           pdb=" CG  LYS B  73 "
           pdb=" CD  LYS B  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.82   55.18     3      1.50e+01 4.44e-03 9.33e+00
  dihedral pdb=" N   PHE B  61 "
           pdb=" CA  PHE B  61 "
           pdb=" CB  PHE B  61 "
           pdb=" CG  PHE B  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    4.96   55.04     3      1.50e+01 4.44e-03 9.32e+00
  ... (remaining 5330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1176
       0.037 -    0.074: 197
       0.074 -    0.111: 84
       0.111 -    0.148: 33
       0.148 -    0.185: 4
  Chirality restraints: 1494
  Sorted by residual:
  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 8.58e-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 8.37e-01
  chirality pdb=" C3'  DC D  77 "
            pdb=" C4'  DC D  77 "
            pdb=" O3'  DC D  77 "
            pdb=" C2'  DC D  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.48   -0.18 2.00e-01 2.50e+01 8.25e-01
  ... (remaining 1491 not shown)

  Planarity restraints: 1322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  58 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B  59 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B  59 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  59 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 168 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.84e+00
        pdb=" C   LEU A 168 "    0.023 2.00e-02 2.50e+03
        pdb=" O   LEU A 168 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLU A 169 "   -0.008 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   7.49e-03 1.40e+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 "   -0.010 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 "   -0.006 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 1319 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 320
        2.68 -     3.24: 8326
        3.24 -     3.79: 13760
        3.79 -     4.35: 17343
        4.35 -     4.90: 26029
  Nonbonded interactions: 65778
  Sorted by model distance:
  nonbonded pdb=" C   TYR A 339 "
            pdb=" OE1 GLN A 340 "
     model   vdw
     2.131 3.270
  nonbonded pdb=" OP2   A C 203 "
            pdb=" N6    A D  50 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" NZ  LYS A 350 "
            pdb=" OE2 GLU A 378 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" N   PHE B  61 "
            pdb=" CD1 PHE B  61 "
     model   vdw
     2.232 3.420
  nonbonded pdb=" O2'   A D  50 "
            pdb=" OP2   G D  52 "
     model   vdw
     2.239 3.040
  ... (remaining 65773 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:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     25.070
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
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   0.057   8893  Z= 0.133
  Angle     :  0.507   6.551  12549  Z= 0.289
  Chirality :  0.039   0.185   1494
  Planarity :  0.003   0.048   1322
  Dihedral  : 16.404  88.022   3547
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  3.57 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -4.46 (0.24), residues: 934
  helix: -1.57 (0.25), residues: 325
  sheet: -4.91 (0.29), residues: 116
  loop : -3.53 (0.25), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.000   TRP A 402 
 HIS   0.001   0.000   HIS B 208 
 PHE   0.007   0.000   PHE A 227 
 TYR   0.004   0.000   TYR A 501 
 ARG   0.001   0.000   ARG A 284 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 149
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 ILE cc_start: 0.8345 (mt) cc_final: 0.7329 (mt)
REVERT: B  401 TRP cc_start: 0.8317 (m100) cc_final: 0.8098 (m100)
  outliers start: 5
  outliers final: 4
  residues processed: 154
  average time/residue: 0.2859
  time to fit residues: 55.8409
Evaluate side-chains
  69 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  96 HIS
A 147 ASN
A 394 GLN
A 478 GLN
A 519 ASN
B  57 ASN
B 145 GLN
B 198 HIS
B 265 ASN
B 330 GLN
B 373 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.078835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.066080 restraints weight = 51117.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.067070 restraints weight = 30626.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.067496 restraints weight = 20903.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   8893  Z= 0.434
  Angle     :  0.711   7.070  12549  Z= 0.365
  Chirality :  0.044   0.171   1494
  Planarity :  0.005   0.047   1322
  Dihedral  : 17.134  74.655   2169
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -4.15 (0.24), residues: 934
  helix: -1.25 (0.26), residues: 334
  sheet: -4.58 (0.24), residues: 171
  loop : -3.15 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A  24 
 HIS   0.004   0.001   HIS A  96 
 PHE   0.015   0.003   PHE A 227 
 TYR   0.021   0.003   TYR B 342 
 ARG   0.008   0.001   ARG B  83 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8914 (pp30) cc_final: 0.8433 (pp30)
REVERT: A  364 ASP cc_start: 0.8287 (p0) cc_final: 0.7205 (p0)
REVERT: B  124 PHE cc_start: 0.8897 (t80) cc_final: 0.8689 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1844
  time to fit residues: 18.5065
Evaluate side-chains
  44 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0010
   chunk 34 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 95 optimal weight:   20.0000
   chunk 57 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 198 HIS
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.081604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.068352 restraints weight = 50908.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.069575 restraints weight = 29967.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.070433 restraints weight = 20582.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8893  Z= 0.139
  Angle     :  0.521   6.735  12549  Z= 0.258
  Chirality :  0.039   0.150   1494
  Planarity :  0.004   0.050   1322
  Dihedral  : 16.928  74.224   2169
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.26), residues: 934
  helix: -0.33 (0.28), residues: 336
  sheet: -3.80 (0.29), residues: 159
  loop : -2.66 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 402 
 HIS   0.006   0.001   HIS A 361 
 PHE   0.013   0.001   PHE A 227 
 TYR   0.015   0.001   TYR A 188 
 ARG   0.006   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8896 (pp30) cc_final: 0.8580 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1712
  time to fit residues: 21.4640
Evaluate side-chains
  52 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 151 GLN
B 198 HIS
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.078399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.065119 restraints weight = 50784.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.066308 restraints weight = 30147.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.067085 restraints weight = 20755.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8893  Z= 0.275
  Angle     :  0.581   7.235  12549  Z= 0.293
  Chirality :  0.040   0.150   1494
  Planarity :  0.004   0.051   1322
  Dihedral  : 17.059  74.454   2169
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.26), residues: 934
  helix: -0.40 (0.28), residues: 332
  sheet: -3.60 (0.30), residues: 170
  loop : -2.44 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 426 
 HIS   0.003   0.001   HIS A 361 
 PHE   0.017   0.002   PHE A 160 
 TYR   0.021   0.002   TYR B 405 
 ARG   0.010   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8861 (pp30) cc_final: 0.8418 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1694
  time to fit residues: 17.0294
Evaluate side-chains
  44 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 94 optimal weight:    9.9990
   chunk 88 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.079520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.066462 restraints weight = 50508.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.067653 restraints weight = 29628.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.068474 restraints weight = 20232.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8893  Z= 0.170
  Angle     :  0.532   6.494  12549  Z= 0.262
  Chirality :  0.039   0.208   1494
  Planarity :  0.004   0.037   1322
  Dihedral  : 16.943  74.239   2169
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.27), residues: 934
  helix: -0.14 (0.29), residues: 334
  sheet: -3.10 (0.33), residues: 158
  loop : -2.26 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 402 
 HIS   0.003   0.001   HIS B 198 
 PHE   0.018   0.002   PHE B 124 
 TYR   0.014   0.001   TYR A 188 
 ARG   0.005   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8829 (pp30) cc_final: 0.8422 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1744
  time to fit residues: 19.0568
Evaluate side-chains
  47 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0030
   chunk 3 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.080551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.067394 restraints weight = 50054.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.068622 restraints weight = 29657.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.069448 restraints weight = 20144.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8893  Z= 0.128
  Angle     :  0.501   6.440  12549  Z= 0.244
  Chirality :  0.038   0.162   1494
  Planarity :  0.004   0.030   1322
  Dihedral  : 16.824  74.107   2169
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.27), residues: 934
  helix:  0.22 (0.30), residues: 332
  sheet: -2.81 (0.34), residues: 158
  loop : -2.09 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 402 
 HIS   0.002   0.001   HIS B 208 
 PHE   0.012   0.001   PHE A 227 
 TYR   0.008   0.001   TYR A 183 
 ARG   0.004   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8855 (pp30) cc_final: 0.8457 (pp30)
REVERT: A  409 THR cc_start: 0.9279 (p) cc_final: 0.9075 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1894
  time to fit residues: 19.8083
Evaluate side-chains
  46 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 77 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0970
   chunk 21 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.080125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.066970 restraints weight = 50527.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.068145 restraints weight = 30084.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.068954 restraints weight = 20686.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8893  Z= 0.145
  Angle     :  0.508   6.553  12549  Z= 0.248
  Chirality :  0.038   0.178   1494
  Planarity :  0.004   0.035   1322
  Dihedral  : 16.804  74.133   2169
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.28), residues: 934
  helix:  0.35 (0.30), residues: 334
  sheet: -2.59 (0.36), residues: 158
  loop : -1.98 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 402 
 HIS   0.002   0.001   HIS B 208 
 PHE   0.013   0.001   PHE A 227 
 TYR   0.023   0.001   TYR B 188 
 ARG   0.006   0.001   ARG B  83 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8860 (pp30) cc_final: 0.8463 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1606
  time to fit residues: 15.3779
Evaluate side-chains
  41 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0980
   chunk 91 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 361 HIS
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.077912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.064678 restraints weight = 51411.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.065828 restraints weight = 30553.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.066588 restraints weight = 20985.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8893  Z= 0.257
  Angle     :  0.581   6.451  12549  Z= 0.293
  Chirality :  0.040   0.164   1494
  Planarity :  0.004   0.034   1322
  Dihedral  : 16.992  74.385   2169
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.27), residues: 934
  helix:  0.06 (0.29), residues: 333
  sheet: -2.56 (0.36), residues: 163
  loop : -2.00 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 426 
 HIS   0.004   0.001   HIS A 361 
 PHE   0.018   0.002   PHE A 160 
 TYR   0.021   0.002   TYR B 405 
 ARG   0.004   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8301 (m-80) cc_final: 0.8054 (m-80)
REVERT: A  182 GLN cc_start: 0.8892 (pp30) cc_final: 0.8458 (pp30)
REVERT: A  364 ASP cc_start: 0.7947 (p0) cc_final: 0.7346 (p0)
REVERT: A  367 GLN cc_start: 0.8540 (mp10) cc_final: 0.8311 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1708
  time to fit residues: 15.1447
Evaluate side-chains
  40 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0270
   chunk 48 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 97 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 18 optimal weight:    0.0030
   chunk 60 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.9652

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

Flipped N/Q/H residues before XYZ refinement:
A 500 GLN
B 265 ASN
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.079246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.066073 restraints weight = 50727.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.067240 restraints weight = 30124.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.068035 restraints weight = 20680.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.4385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8893  Z= 0.140
  Angle     :  0.515   7.297  12549  Z= 0.253
  Chirality :  0.038   0.153   1494
  Planarity :  0.004   0.036   1322
  Dihedral  : 16.872  74.127   2169
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.28), residues: 934
  helix:  0.29 (0.30), residues: 334
  sheet: -2.24 (0.37), residues: 156
  loop : -1.84 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 402 
 HIS   0.002   0.001   HIS B 208 
 PHE   0.012   0.001   PHE A 227 
 TYR   0.014   0.001   TYR A 188 
 ARG   0.004   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8860 (pp30) cc_final: 0.8448 (pp30)
REVERT: A  364 ASP cc_start: 0.8038 (p0) cc_final: 0.7479 (p0)
REVERT: A  367 GLN cc_start: 0.8567 (mp10) cc_final: 0.8306 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1650
  time to fit residues: 16.6804
Evaluate side-chains
  44 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    3.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 361 HIS
B 265 ASN
B 348 ASN
B 373 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.076697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.063448 restraints weight = 51140.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.064565 restraints weight = 30879.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.065292 restraints weight = 21483.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8893  Z= 0.333
  Angle     :  0.626   6.649  12549  Z= 0.317
  Chirality :  0.041   0.147   1494
  Planarity :  0.004   0.033   1322
  Dihedral  : 17.171  74.482   2169
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.27), residues: 934
  helix: -0.04 (0.29), residues: 333
  sheet: -2.39 (0.38), residues: 163
  loop : -1.91 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  88 
 HIS   0.002   0.001   HIS A 361 
 PHE   0.023   0.002   PHE A 160 
 TYR   0.028   0.002   TYR B 405 
 ARG   0.004   0.001   ARG B  78 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 GLN cc_start: 0.8915 (pp30) cc_final: 0.8460 (pp30)
REVERT: A  364 ASP cc_start: 0.8078 (p0) cc_final: 0.7523 (p0)
REVERT: A  367 GLN cc_start: 0.8524 (mp10) cc_final: 0.8283 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1878
  time to fit residues: 14.8614
Evaluate side-chains
  37 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 265 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.078353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.065221 restraints weight = 51012.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.066362 restraints weight = 30081.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.067136 restraints weight = 20763.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8893  Z= 0.151
  Angle     :  0.529   7.341  12549  Z= 0.262
  Chirality :  0.038   0.152   1494
  Planarity :  0.004   0.035   1322
  Dihedral  : 17.002  74.179   2169
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.28), residues: 934
  helix:  0.24 (0.29), residues: 334
  sheet: -2.13 (0.38), residues: 156
  loop : -1.81 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 402 
 HIS   0.003   0.001   HIS B 208 
 PHE   0.018   0.002   PHE B 346 
 TYR   0.015   0.001   TYR A 188 
 ARG   0.004   0.001   ARG B  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2257.18 seconds
wall clock time: 41 minutes 21.84 seconds (2481.84 seconds total)