Starting phenix.real_space_refine
on Fri Jul 25 12:55:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u2b_26311/07_2025/7u2b_26311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2b_26311/07_2025/7u2b_26311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2025/7u2b_26311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2025/7u2b_26311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2025/7u2b_26311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2025/7u2b_26311.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      53      5.49       5
     S      34      5.16       5
     C    4408      2.51       5
     N    1316      2.21       5
     O    1505      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7316
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1111
          Classifications: {'RNA': 53}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 5, 'rna3p': 47}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'  A%rna2p_pur:plan2': 1, '  A%rna2p_pur:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 2500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2500
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3647
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SSA%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SSA%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 4.66, per 1000 atoms: 0.64
  Number of scatterers: 7316
  At special positions: 0
  Unit cell: (70.15, 95.45, 126.5, 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      34     16.00
     P      53     15.00
     O    1505      8.00
     N    1316      7.00
     C    4408      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: 1.96
  Conformation dependent library (CDL) restraints added in 699.1 milliseconds
  

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      42.8% alpha, 16.0% beta
      8 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 2.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 233 through 253
      removed outlier: 3.507A  pdb=" N   ARG A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 272
      removed outlier: 3.579A  pdb=" N   PHE A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 308
      removed outlier: 4.020A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
      removed outlier: 3.512A  pdb=" N   SER A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 434
    Processing helix  chain 'A' and resid 457 through 468
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 4.254A  pdb=" N   SER A 483 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TYR A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 3.659A  pdb=" N   GLU B  46 " --> pdb=" O   ASN B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 64
      removed outlier: 3.595A  pdb=" N   PHE B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.613A  pdb=" N   ALA B  70 " --> pdb=" O   CYS B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 84
      No H-bonds generated for 'chain 'B' and resid 82 through 84'
    Processing helix  chain 'B' and resid 85 through 123
      removed outlier: 3.610A  pdb=" N   ILE B  89 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 132
    Processing helix  chain 'B' and resid 132 through 169
      removed outlier: 3.592A  pdb=" N   GLN B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
      removed outlier: 4.311A  pdb=" N   LYS B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 233 through 253
    Processing helix  chain 'B' and resid 265 through 273
      removed outlier: 3.619A  pdb=" N   PHE B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.731A  pdb=" N   GLY B 303 " --> pdb=" O   THR B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 383
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.657A  pdb=" N   ARG B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 469
    Processing helix  chain 'B' and resid 478 through 486
      removed outlier: 4.076A  pdb=" N   SER B 483 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   TYR B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
      removed outlier: 6.402A  pdb=" N   VAL A 188 " --> pdb=" O   ASP A 390 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ASP A 390 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 9.763A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASN A 451 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS A 350 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   SER A 326 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 325 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU B 231 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR B 230 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.702A  pdb=" N   TYR A 230 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER B 326 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 350 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA B 408 " --> pdb=" O   GLU B 418 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   VAL B 188 " --> pdb=" O   ASP B 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264
    Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 312
    Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438
    Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500
      removed outlier: 3.539A  pdb=" N   GLN A 499 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   HIS B 311 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   GLN B 438 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL B 313 " --> pdb=" O   GLN B 438 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264

    291 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      40 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2090
        1.33 -     1.45: 1486
        1.45 -     1.57: 3841
        1.57 -     1.69: 112
        1.69 -     1.81: 56
  Bond restraints: 7585
  Sorted by residual:
  bond pdb=" C6  SSA B 601 "
       pdb=" N6  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.520 -0.187 2.00e-02 2.50e+03 8.77e+01
  bond pdb=" C6  SSA A 601 "
       pdb=" N6  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.519 -0.186 2.00e-02 2.50e+03 8.63e+01
  bond pdb=" O5' SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.731 -0.150 2.00e-02 2.50e+03 5.62e+01
  bond pdb=" O2S SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.584 -0.149 2.00e-02 2.50e+03 5.58e+01
  bond pdb=" O2S SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.581 -0.146 2.00e-02 2.50e+03 5.32e+01
  ... (remaining 7580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 10455
        4.02 -     8.04: 61
        8.04 -    12.06: 7
       12.06 -    16.08: 0
       16.08 -    20.10: 2
  Bond angle restraints: 10525
  Sorted by residual:
  angle pdb=" O1S SSA B 601 "
        pdb=" S1  SSA B 601 "
        pdb=" O2S SSA B 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.24   20.10 3.00e+00 1.11e-01 4.49e+01
  angle pdb=" O1S SSA A 601 "
        pdb=" S1  SSA A 601 "
        pdb=" O2S SSA A 601 "
      ideal   model   delta    sigma   weight residual
     121.34  102.90   18.44 3.00e+00 1.11e-01 3.78e+01
  angle pdb=" N   THR B 426 "
        pdb=" CA  THR B 426 "
        pdb=" C   THR B 426 "
      ideal   model   delta    sigma   weight residual
     111.37  117.25   -5.88 1.64e+00 3.72e-01 1.28e+01
  angle pdb=" N1  SSA B 601 "
        pdb=" C6  SSA B 601 "
        pdb=" N6  SSA B 601 "
      ideal   model   delta    sigma   weight residual
     119.38  108.72   10.66 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" N   VAL B 223 "
        pdb=" CA  VAL B 223 "
        pdb=" C   VAL B 223 "
      ideal   model   delta    sigma   weight residual
     109.34  116.64   -7.30 2.08e+00 2.31e-01 1.23e+01
  ... (remaining 10520 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.30: 4362
       30.30 -    60.61: 225
       60.61 -    90.91: 66
       90.91 -   121.22: 1
      121.22 -   151.52: 3
  Dihedral angle restraints: 4657
    sinusoidal: 2419
      harmonic: 2238
  Sorted by residual:
  dihedral pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
           pdb=" N1    U C   9 "
           pdb=" C2    U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -8.48 -151.52     1      1.50e+01 4.44e-03 8.02e+01
  dihedral pdb=" O4'   C C   8 "
           pdb=" C1'   C C   8 "
           pdb=" N1    C C   8 "
           pdb=" C2    C C   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -10.64 -149.36     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   C C  10 "
           pdb=" C1'   C C  10 "
           pdb=" N1    C C  10 "
           pdb=" C2    C C  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -16.50 -143.50     1      1.50e+01 4.44e-03 7.70e+01
  ... (remaining 4654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1164
       0.113 -    0.226: 36
       0.226 -    0.339: 2
       0.339 -    0.453: 0
       0.453 -    0.566: 2
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CA  SSA B 601 "
            pdb=" CB  SSA B 601 "
            pdb=" C9  SSA B 601 "
            pdb=" N10 SSA B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.03    0.57 2.00e-01 2.50e+01 8.00e+00
  chirality pdb=" CA  SSA A 601 "
            pdb=" CB  SSA A 601 "
            pdb=" C9  SSA A 601 "
            pdb=" N10 SSA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.02    0.56 2.00e-01 2.50e+01 7.75e+00
  chirality pdb=" C3' SSA B 601 "
            pdb=" C2' SSA B 601 "
            pdb=" C4' SSA B 601 "
            pdb=" O3' SSA B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.49   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  45 "   -0.030 2.00e-02 2.50e+03   1.43e-02 5.64e+00
        pdb=" N9    A C  45 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    A C  45 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A C  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A C  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A C  45 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A C  45 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A C  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A C  45 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A C  45 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A C  45 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 457 "   -0.029 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO B 458 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 458 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 458 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 457 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 458 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 458 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 458 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 43
        2.53 -     3.12: 5593
        3.12 -     3.71: 11574
        3.71 -     4.31: 15512
        4.31 -     4.90: 25209
  Nonbonded interactions: 57931
  Sorted by model distance:
  nonbonded pdb=" O2    C C   8 "
            pdb=" O2'   C C  33 "
     model   vdw
     1.936 3.040
  nonbonded pdb=" O2'   A C  45 "
            pdb=" O5'   A C  46 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OG1 THR A 453 "
            pdb=" OG  SSA A 601 "
     model   vdw
     2.032 3.040
  nonbonded pdb=" OG  SER A 224 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" OH  TYR A 329 "
            pdb=" OH  TYR B 329 "
     model   vdw
     2.099 3.040
  ... (remaining 57926 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:             0.290
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.240
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
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      :  0.009   0.187   7585  Z= 0.456
  Angle     :  0.973  20.098  10525  Z= 0.522
  Chirality :  0.053   0.566   1204
  Planarity :  0.004   0.043   1184
  Dihedral  : 18.721 151.523   3219
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 12.52 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  2.20 (0.29), residues: 772
  helix:  3.12 (0.28), residues: 288
  sheet:  0.78 (0.48), residues: 105
  loop :  0.40 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 409 
 HIS   0.005   0.001   HIS A 240 
 PHE   0.022   0.002   PHE B 404 
 TYR   0.014   0.002   TYR B 230 
 ARG   0.010   0.001   ARG B 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15712 (  311)
  hydrogen bonds       : angle       6.87084 (  883)
  covalent geometry    : bond        0.00940 ( 7585)
  covalent geometry    : angle       0.97297 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 236
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 MET cc_start: 0.8547 (mtt) cc_final: 0.8124 (mmm)
REVERT: A  205 HIS cc_start: 0.8447 (p-80) cc_final: 0.8172 (p-80)
REVERT: A  211 LYS cc_start: 0.8708 (mtmp) cc_final: 0.8225 (tmtt)
REVERT: A  218 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7820 (mmmm)
REVERT: A  258 MET cc_start: 0.8254 (ttm) cc_final: 0.7646 (mtp)
REVERT: A  425 CYS cc_start: 0.8546 (m) cc_final: 0.8241 (t)
REVERT: A  451 ASN cc_start: 0.8559 (p0) cc_final: 0.7950 (p0)
REVERT: A  468 ASN cc_start: 0.8250 (m-40) cc_final: 0.7814 (m-40)
REVERT: A  477 VAL cc_start: 0.8386 (t) cc_final: 0.8156 (p)
REVERT: A  482 GLN cc_start: 0.8187 (mt0) cc_final: 0.7896 (pp30)
REVERT: B  153 TYR cc_start: 0.8243 (m-80) cc_final: 0.7590 (m-80)
REVERT: B  248 ASN cc_start: 0.7962 (m-40) cc_final: 0.7322 (t0)
REVERT: B  252 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8546 (ttp-110)
REVERT: B  256 THR cc_start: 0.7597 (m) cc_final: 0.6740 (p)
REVERT: B  326 SER cc_start: 0.8804 (p) cc_final: 0.8521 (t)
REVERT: B  366 GLN cc_start: 0.6857 (tt0) cc_final: 0.6395 (tm-30)
REVERT: B  437 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6557 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2323
  time to fit residues: 69.7901
Evaluate side-chains
  114 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN
A 375 GLN
A 448 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 ASN
B 438 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107791 restraints weight = 11680.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.110426 restraints weight = 6464.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112168 restraints weight = 4229.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7585  Z= 0.141
  Angle     :  0.638   6.989  10525  Z= 0.318
  Chirality :  0.039   0.157   1204
  Planarity :  0.005   0.084   1184
  Dihedral  : 18.462 161.928   1721
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.82 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  2.04 (0.29), residues: 772
  helix:  2.54 (0.29), residues: 301
  sheet:  1.18 (0.49), residues: 99
  loop :  0.49 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.007   0.001   HIS B 434 
 PHE   0.023   0.002   PHE B 247 
 TYR   0.035   0.003   TYR B  47 
 ARG   0.006   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05022 (  311)
  hydrogen bonds       : angle       5.31074 (  883)
  covalent geometry    : bond        0.00301 ( 7585)
  covalent geometry    : angle       0.63787 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8095 (tmtt)
REVERT: A  258 MET cc_start: 0.7178 (ttm) cc_final: 0.6875 (mtp)
REVERT: A  264 LEU cc_start: 0.9169 (mm) cc_final: 0.8931 (mp)
REVERT: A  350 LYS cc_start: 0.8581 (ptmm) cc_final: 0.8278 (ptmt)
REVERT: A  405 ASP cc_start: 0.7722 (m-30) cc_final: 0.7462 (m-30)
REVERT: A  429 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7964 (mp10)
REVERT: A  482 GLN cc_start: 0.8220 (mt0) cc_final: 0.7956 (tm-30)
REVERT: B  130 GLN cc_start: 0.8476 (mt0) cc_final: 0.7805 (tm-30)
REVERT: B  153 TYR cc_start: 0.8600 (m-80) cc_final: 0.8322 (m-80)
REVERT: B  248 ASN cc_start: 0.7946 (m-40) cc_final: 0.7479 (t0)
REVERT: B  326 SER cc_start: 0.8874 (p) cc_final: 0.8557 (p)
REVERT: B  348 PHE cc_start: 0.8271 (p90) cc_final: 0.7921 (p90)
REVERT: B  353 MET cc_start: 0.7620 (mtp) cc_final: 0.7196 (mtp)
REVERT: B  366 GLN cc_start: 0.7703 (tt0) cc_final: 0.7324 (tm-30)
REVERT: B  395 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7401 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2062
  time to fit residues: 49.1343
Evaluate side-chains
  110 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0170
   chunk 53 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
A 347 HIS
A 469 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.133631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107095 restraints weight = 11662.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.109602 restraints weight = 6551.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111246 restraints weight = 4325.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7585  Z= 0.122
  Angle     :  0.570   6.601  10525  Z= 0.284
  Chirality :  0.038   0.172   1204
  Planarity :  0.004   0.031   1184
  Dihedral  : 18.060 167.806   1721
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.95 (0.30), residues: 772
  helix:  2.32 (0.30), residues: 302
  sheet:  1.18 (0.48), residues: 103
  loop :  0.56 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.008   0.001   HIS A 226 
 PHE   0.018   0.001   PHE B 247 
 TYR   0.015   0.002   TYR B 307 
 ARG   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  311)
  hydrogen bonds       : angle       4.93759 (  883)
  covalent geometry    : bond        0.00259 ( 7585)
  covalent geometry    : angle       0.56979 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8444 (tmtt)
REVERT: A  258 MET cc_start: 0.7287 (ttm) cc_final: 0.6921 (mtp)
REVERT: A  350 LYS cc_start: 0.8746 (ptmm) cc_final: 0.8454 (ptmt)
REVERT: A  405 ASP cc_start: 0.7605 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  429 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7964 (mp10)
REVERT: B  130 GLN cc_start: 0.8355 (mt0) cc_final: 0.7763 (tm-30)
REVERT: B  153 TYR cc_start: 0.8549 (m-80) cc_final: 0.8312 (m-80)
REVERT: B  326 SER cc_start: 0.8917 (p) cc_final: 0.8380 (t)
REVERT: B  348 PHE cc_start: 0.8292 (p90) cc_final: 0.8039 (p90)
REVERT: B  353 MET cc_start: 0.7568 (mtp) cc_final: 0.7137 (mtt)
REVERT: B  366 GLN cc_start: 0.7610 (tt0) cc_final: 0.7358 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2059
  time to fit residues: 44.3919
Evaluate side-chains
  107 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
** A 469 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.131858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.104439 restraints weight = 11955.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.106963 restraints weight = 6768.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.108553 restraints weight = 4487.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7585  Z= 0.129
  Angle     :  0.574   7.930  10525  Z= 0.287
  Chirality :  0.038   0.147   1204
  Planarity :  0.004   0.030   1184
  Dihedral  : 17.802 174.561   1721
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.86 (0.30), residues: 772
  helix:  2.25 (0.31), residues: 302
  sheet:  1.37 (0.50), residues: 92
  loop :  0.44 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.016   0.001   PHE B 247 
 TYR   0.022   0.002   TYR B  52 
 ARG   0.006   0.000   ARG B 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  311)
  hydrogen bonds       : angle       4.81183 (  883)
  covalent geometry    : bond        0.00285 ( 7585)
  covalent geometry    : angle       0.57440 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8378 (tptp)
REVERT: A  218 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8460 (mmmm)
REVERT: A  258 MET cc_start: 0.7298 (ttm) cc_final: 0.6992 (mtp)
REVERT: A  429 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7955 (mp10)
REVERT: A  453 THR cc_start: 0.8942 (m) cc_final: 0.8733 (p)
REVERT: B   52 TYR cc_start: 0.8427 (m-80) cc_final: 0.8217 (m-10)
REVERT: B  130 GLN cc_start: 0.8397 (mt0) cc_final: 0.7771 (tm-30)
REVERT: B  326 SER cc_start: 0.9002 (p) cc_final: 0.8511 (t)
REVERT: B  347 HIS cc_start: 0.7967 (p-80) cc_final: 0.7757 (p-80)
REVERT: B  353 MET cc_start: 0.7452 (mtp) cc_final: 0.7069 (mtm)
REVERT: B  366 GLN cc_start: 0.7664 (tt0) cc_final: 0.7358 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1898
  time to fit residues: 37.3562
Evaluate side-chains
  103 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 78 optimal weight:    0.0980
   chunk 65 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 59 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.132425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.105383 restraints weight = 11892.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107881 restraints weight = 6706.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109517 restraints weight = 4446.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7585  Z= 0.112
  Angle     :  0.549   8.902  10525  Z= 0.275
  Chirality :  0.038   0.147   1204
  Planarity :  0.003   0.026   1184
  Dihedral  : 17.475 179.449   1721
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.87 (0.30), residues: 772
  helix:  2.28 (0.31), residues: 303
  sheet:  1.35 (0.50), residues: 92
  loop :  0.43 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.014   0.001   PHE A 247 
 TYR   0.019   0.002   TYR B  52 
 ARG   0.005   0.000   ARG B 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  311)
  hydrogen bonds       : angle       4.69560 (  883)
  covalent geometry    : bond        0.00244 ( 7585)
  covalent geometry    : angle       0.54920 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8415 (tptp)
REVERT: A  218 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8469 (mmmm)
REVERT: A  258 MET cc_start: 0.7318 (ttm) cc_final: 0.7040 (mtp)
REVERT: A  429 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7939 (mp10)
REVERT: A  453 THR cc_start: 0.8857 (m) cc_final: 0.8614 (p)
REVERT: B  130 GLN cc_start: 0.8230 (mt0) cc_final: 0.7632 (tm-30)
REVERT: B  326 SER cc_start: 0.9064 (p) cc_final: 0.8625 (t)
REVERT: B  347 HIS cc_start: 0.8001 (p-80) cc_final: 0.7791 (p-80)
REVERT: B  353 MET cc_start: 0.7393 (mtp) cc_final: 0.7036 (mtm)
REVERT: B  366 GLN cc_start: 0.7720 (tt0) cc_final: 0.7367 (tm-30)
REVERT: B  410 MET cc_start: 0.8897 (mpp) cc_final: 0.8672 (mpp)
REVERT: B  436 MET cc_start: 0.7500 (ttp) cc_final: 0.6798 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1837
  time to fit residues: 35.1828
Evaluate side-chains
  102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 347 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.128183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.101134 restraints weight = 12115.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.103509 restraints weight = 6977.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.105051 restraints weight = 4691.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7585  Z= 0.157
  Angle     :  0.600   7.828  10525  Z= 0.301
  Chirality :  0.039   0.167   1204
  Planarity :  0.004   0.025   1184
  Dihedral  : 17.280 177.539   1721
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.74 (0.30), residues: 772
  helix:  2.10 (0.31), residues: 303
  sheet:  1.32 (0.54), residues: 94
  loop :  0.40 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  93 
 HIS   0.004   0.001   HIS B 385 
 PHE   0.022   0.002   PHE B 308 
 TYR   0.014   0.002   TYR B 307 
 ARG   0.004   0.001   ARG B 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  311)
  hydrogen bonds       : angle       4.74549 (  883)
  covalent geometry    : bond        0.00351 ( 7585)
  covalent geometry    : angle       0.59950 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8483 (tptp)
REVERT: A  242 LEU cc_start: 0.8334 (mt) cc_final: 0.8108 (tp)
REVERT: A  258 MET cc_start: 0.7430 (ttm) cc_final: 0.7162 (mtp)
REVERT: A  429 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7821 (mp10)
REVERT: A  453 THR cc_start: 0.8823 (m) cc_final: 0.8591 (p)
REVERT: B  118 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7177 (ttp80)
REVERT: B  144 GLU cc_start: 0.7675 (tp30) cc_final: 0.7439 (tp30)
REVERT: B  366 GLN cc_start: 0.7727 (tt0) cc_final: 0.7406 (tm-30)
REVERT: B  391 MET cc_start: 0.7475 (tpp) cc_final: 0.7135 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2043
  time to fit residues: 39.4876
Evaluate side-chains
  103 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 78 optimal weight:    0.4980
   chunk 70 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.135100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107367 restraints weight = 11611.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.109898 restraints weight = 6658.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111520 restraints weight = 4435.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7585  Z= 0.111
  Angle     :  0.563   7.179  10525  Z= 0.283
  Chirality :  0.039   0.294   1204
  Planarity :  0.003   0.023   1184
  Dihedral  : 17.175 177.600   1721
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.72 (0.30), residues: 772
  helix:  2.14 (0.31), residues: 302
  sheet:  1.07 (0.52), residues: 94
  loop :  0.42 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.015   0.001   PHE B 247 
 TYR   0.019   0.002   TYR B 401 
 ARG   0.004   0.000   ARG B 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  311)
  hydrogen bonds       : angle       4.72692 (  883)
  covalent geometry    : bond        0.00243 ( 7585)
  covalent geometry    : angle       0.56331 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.7321 (ttm) cc_final: 0.7119 (mtp)
REVERT: A  389 LEU cc_start: 0.8736 (pp) cc_final: 0.8515 (pp)
REVERT: A  429 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8009 (mp10)
REVERT: A  453 THR cc_start: 0.8792 (m) cc_final: 0.8558 (p)
REVERT: B  118 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7235 (ttp80)
REVERT: B  250 LEU cc_start: 0.9101 (mm) cc_final: 0.8540 (mt)
REVERT: B  296 LEU cc_start: 0.8803 (mt) cc_final: 0.8493 (mp)
REVERT: B  352 GLU cc_start: 0.8106 (tp30) cc_final: 0.7811 (tp30)
REVERT: B  366 GLN cc_start: 0.7714 (tt0) cc_final: 0.7391 (tm-30)
REVERT: B  436 MET cc_start: 0.7607 (ttp) cc_final: 0.7294 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.2402
  time to fit residues: 49.1570
Evaluate side-chains
  104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 60 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 217 GLN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.133491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.105183 restraints weight = 11935.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107680 restraints weight = 6856.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109239 restraints weight = 4656.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7585  Z= 0.144
  Angle     :  0.582   6.613  10525  Z= 0.295
  Chirality :  0.040   0.216   1204
  Planarity :  0.004   0.032   1184
  Dihedral  : 17.100 175.266   1721
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.59 (0.30), residues: 772
  helix:  2.06 (0.31), residues: 302
  sheet:  1.02 (0.53), residues: 94
  loop :  0.32 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.008   0.001   HIS B 347 
 PHE   0.017   0.002   PHE B 371 
 TYR   0.018   0.002   TYR B  52 
 ARG   0.005   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  311)
  hydrogen bonds       : angle       4.79341 (  883)
  covalent geometry    : bond        0.00326 ( 7585)
  covalent geometry    : angle       0.58244 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  429 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7876 (mp10)
REVERT: B  118 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7220 (ttp80)
REVERT: B  144 GLU cc_start: 0.7717 (tp30) cc_final: 0.7435 (tp30)
REVERT: B  366 GLN cc_start: 0.7623 (tt0) cc_final: 0.7378 (tm-30)
REVERT: B  377 GLU cc_start: 0.7924 (tp30) cc_final: 0.7479 (tp30)
REVERT: B  436 MET cc_start: 0.7370 (ttp) cc_final: 0.6851 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1747
  time to fit residues: 33.7994
Evaluate side-chains
  101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    0.0270
   chunk 62 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:   10.0000
   chunk 79 optimal weight:    0.2980
   chunk 39 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.107246 restraints weight = 11794.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.109719 restraints weight = 6931.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.111340 restraints weight = 4729.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7585  Z= 0.110
  Angle     :  0.574   7.029  10525  Z= 0.288
  Chirality :  0.039   0.176   1204
  Planarity :  0.003   0.026   1184
  Dihedral  : 17.002 175.167   1721
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.53 (0.30), residues: 772
  helix:  2.03 (0.31), residues: 304
  sheet:  1.01 (0.51), residues: 92
  loop :  0.24 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.014   0.001   PHE B 247 
 TYR   0.013   0.001   TYR B  52 
 ARG   0.004   0.000   ARG B 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  311)
  hydrogen bonds       : angle       4.76510 (  883)
  covalent geometry    : bond        0.00242 ( 7585)
  covalent geometry    : angle       0.57448 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  429 GLN cc_start: 0.8221 (mm-40) cc_final: 0.8000 (mp10)
REVERT: B  118 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7248 (ttp80)
REVERT: B  258 MET cc_start: 0.8364 (mtp) cc_final: 0.8072 (mtp)
REVERT: B  290 ARG cc_start: 0.8175 (tpm170) cc_final: 0.7855 (tpm170)
REVERT: B  352 GLU cc_start: 0.8114 (tp30) cc_final: 0.7640 (tp30)
REVERT: B  366 GLN cc_start: 0.7570 (tt0) cc_final: 0.7314 (tm-30)
REVERT: B  436 MET cc_start: 0.7358 (ttp) cc_final: 0.7043 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1720
  time to fit residues: 32.4969
Evaluate side-chains
  98 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0270
   chunk 26 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 53 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
** A 469 GLN ** 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 = 0.3787 r_free = 0.3787 target = 0.136528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.108079 restraints weight = 11868.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.110556 restraints weight = 6920.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.112096 restraints weight = 4693.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7585  Z= 0.110
  Angle     :  0.566   8.059  10525  Z= 0.284
  Chirality :  0.039   0.171   1204
  Planarity :  0.004   0.027   1184
  Dihedral  : 16.914 173.773   1721
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.55 (0.30), residues: 772
  helix:  2.06 (0.31), residues: 303
  sheet:  1.01 (0.50), residues: 91
  loop :  0.27 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 409 
 HIS   0.010   0.001   HIS A 222 
 PHE   0.042   0.002   PHE A 255 
 TYR   0.026   0.002   TYR B 153 
 ARG   0.007   0.000   ARG B 344 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03302 (  311)
  hydrogen bonds       : angle       4.73977 (  883)
  covalent geometry    : bond        0.00247 ( 7585)
  covalent geometry    : angle       0.56596 (10525)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.675 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7192 (ttp80)
REVERT: B  258 MET cc_start: 0.8338 (mtp) cc_final: 0.8068 (mtp)
REVERT: B  352 GLU cc_start: 0.8148 (tp30) cc_final: 0.7675 (tp30)
REVERT: B  366 GLN cc_start: 0.7547 (tt0) cc_final: 0.7269 (tm-30)
REVERT: B  436 MET cc_start: 0.7357 (ttp) cc_final: 0.6987 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1953
  time to fit residues: 36.4010
Evaluate side-chains
  95 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0870
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.131527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103667 restraints weight = 11935.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.105991 restraints weight = 7035.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107592 restraints weight = 4840.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.5064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7585  Z= 0.164
  Angle     :  0.602   9.339  10525  Z= 0.305
  Chirality :  0.040   0.148   1204
  Planarity :  0.004   0.034   1184
  Dihedral  : 16.997 170.354   1721
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  1.27 (0.30), residues: 772
  helix:  1.87 (0.31), residues: 301
  sheet:  0.66 (0.51), residues: 92
  loop :  0.12 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.010   0.001   HIS A 222 
 PHE   0.023   0.002   PHE A 255 
 TYR   0.024   0.002   TYR A 230 
 ARG   0.008   0.001   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  311)
  hydrogen bonds       : angle       4.86586 (  883)
  covalent geometry    : bond        0.00375 ( 7585)
  covalent geometry    : angle       0.60151 (10525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2387.41 seconds
wall clock time: 42 minutes 45.74 seconds (2565.74 seconds total)