Starting phenix.real_space_refine
on Fri Jul 25 06:50:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u2a_26310/07_2025/7u2a_26310.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2a_26310/07_2025/7u2a_26310.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/7u2a_26310/07_2025/7u2a_26310.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2025/7u2a_26310.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2025/7u2a_26310.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2025/7u2a_26310.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=   0.010
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      38      5.49       5
     S      34      5.16       5
     C    4179      2.51       5
     N    1233      2.21       5
     O    1371      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 87 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: 6855
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 794
          Classifications: {'RNA': 38}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 15, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 2, 'rna3p': 35}
          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: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3503
          Classifications: {'peptide': 442}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 415}
          Chain breaks: 2
          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: 4.75, per 1000 atoms: 0.69
  Number of scatterers: 6855
  At special positions: 0
  Unit cell: (70.15, 83.95, 117.3, 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      38     15.00
     O    1371      8.00
     N    1233      7.00
     C    4179      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: 2.06
  Conformation dependent library (CDL) restraints added in 748.3 milliseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      42.2% alpha, 16.7% beta
      10 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 2.30
  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
    Processing helix  chain 'A' and resid 266 through 272
    Processing helix  chain 'A' and resid 299 through 308
      removed outlier: 4.156A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
    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: 4.296A  pdb=" N   SER A 483 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   TYR A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 3.737A  pdb=" N   GLU B  46 " --> pdb=" O   ASN B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 65
      removed outlier: 4.354A  pdb=" N   ALA B  65 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.605A  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 118
      removed outlier: 3.724A  pdb=" N   ILE B  89 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 169
      Proline residue:  B 154  - end of helix
      removed outlier: 4.233A  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 254
    Processing helix  chain 'B' and resid 266 through 273
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.888A  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 392 through 397
      removed outlier: 4.546A  pdb=" N   GLY B 397 " --> pdb=" O   THR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.546A  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: 3.813A  pdb=" N   SER B 483 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   TYR B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192
      removed outlier: 6.262A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY A 417 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASN A 451 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS A 350 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   SER A 326 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   SER A 325 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 231 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.735A  pdb=" N   TYR A 230 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER B 326 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS B 350 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.309A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE B 406 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER B 421 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   PHE B 404 " --> pdb=" O   SER B 421 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 5.640A  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 265
    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: 5.869A  pdb=" N   HIS B 311 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   GLN B 438 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
      removed outlier: 6.164A  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 265

    282 hydrogen bonds defined for protein.
    813 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 2.38 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: 1888
        1.33 -     1.45: 1429
        1.45 -     1.57: 3629
        1.57 -     1.69: 82
        1.69 -     1.81: 56
  Bond restraints: 7084
  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  1.514 -0.181 2.00e-02 2.50e+03 8.18e+01
  bond pdb=" O5' SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.730 -0.149 2.00e-02 2.50e+03 5.55e+01
  bond pdb=" O2S SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.583 -0.148 2.00e-02 2.50e+03 5.46e+01
  bond pdb=" O2S SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.579 -0.144 2.00e-02 2.50e+03 5.17e+01
  ... (remaining 7079 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.79: 9667
        3.79 -     7.59: 93
        7.59 -    11.38: 11
       11.38 -    15.17: 0
       15.17 -    18.97: 2
  Bond angle restraints: 9773
  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  102.37   18.97 3.00e+00 1.11e-01 4.00e+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  102.72   18.62 3.00e+00 1.11e-01 3.85e+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  108.60   10.78 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" N1  SSA A 601 "
        pdb=" C6  SSA A 601 "
        pdb=" N6  SSA A 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   PHE B 386 "
        pdb=" CA  PHE B 386 "
        pdb=" C   PHE B 386 "
      ideal   model   delta    sigma   weight residual
     109.24  114.98   -5.74 1.67e+00 3.59e-01 1.18e+01
  ... (remaining 9768 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.35: 4074
       30.35 -    60.71: 207
       60.71 -    91.06: 52
       91.06 -   121.41: 1
      121.41 -   151.76: 2
  Dihedral angle restraints: 4336
    sinusoidal: 2153
      harmonic: 2183
  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   -8.24 -151.76     1      1.50e+01 4.44e-03 8.03e+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  -10.36 -149.64     1      1.50e+01 4.44e-03 7.95e+01
  dihedral pdb=" O4'   A C  45 "
           pdb=" C1'   A C  45 "
           pdb=" N9    A C  45 "
           pdb=" C4    A C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -173.42   67.42     1      1.70e+01 3.46e-03 2.05e+01
  ... (remaining 4333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1071
       0.118 -    0.235: 35
       0.235 -    0.353: 1
       0.353 -    0.470: 0
       0.470 -    0.588: 2
  Chirality restraints: 1109
  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   -3.06    0.59 2.00e-01 2.50e+01 8.64e+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   -3.03    0.57 2.00e-01 2.50e+01 8.01e+00
  chirality pdb=" C3' SSA A 601 "
            pdb=" C2' SSA A 601 "
            pdb=" C4' SSA A 601 "
            pdb=" O3' SSA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.48   -0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1106 not shown)

  Planarity restraints: 1139
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 221 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.49e+00
        pdb=" C   SER B 221 "    0.041 2.00e-02 2.50e+03
        pdb=" O   SER B 221 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   HIS B 222 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  45 "   -0.028 2.00e-02 2.50e+03   1.33e-02 4.87e+00
        pdb=" N9    A C  45 "    0.032 2.00e-02 2.50e+03
        pdb=" C8    A C  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A C  45 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A C  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A C  45 "   -0.004 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 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A C  45 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 347 "   -0.014 2.00e-02 2.50e+03   1.50e-02 3.37e+00
        pdb=" CG  HIS B 347 "    0.032 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 347 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 347 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 347 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 347 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1136 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 49
        2.51 -     3.11: 5218
        3.11 -     3.71: 10911
        3.71 -     4.30: 14874
        4.30 -     4.90: 24178
  Nonbonded interactions: 55230
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 329 "
            pdb=" OH  TYR B 329 "
     model   vdw
     1.918 3.040
  nonbonded pdb=" OG  SSA A 601 "
            pdb=" O9  SSA A 601 "
     model   vdw
     2.005 3.040
  nonbonded pdb=" OD1 ASN B 451 "
            pdb=" OG  SSA B 601 "
     model   vdw
     2.019 3.040
  nonbonded pdb=" OG  SER A 224 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.020 3.040
  nonbonded pdb=" O2'   A C  45 "
            pdb=" O5'   A C  46 "
     model   vdw
     2.039 3.040
  ... (remaining 55225 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:             0.220
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.940
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
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      :  0.010   0.187   7084  Z= 0.483
  Angle     :  1.056  18.967   9773  Z= 0.571
  Chirality :  0.057   0.588   1109
  Planarity :  0.004   0.045   1139
  Dihedral  : 18.248 151.765   2932
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 12.66 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: 751
  helix:  2.82 (0.29), residues: 296
  sheet:  1.13 (0.54), residues: 87
  loop :  0.23 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 409 
 HIS   0.016   0.002   HIS B 347 
 PHE   0.019   0.002   PHE B 404 
 TYR   0.019   0.003   TYR B 230 
 ARG   0.006   0.001   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15500 (  307)
  hydrogen bonds       : angle       7.04915 (  863)
  covalent geometry    : bond        0.01004 ( 7084)
  covalent geometry    : angle       1.05603 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 262
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 MET cc_start: 0.8645 (mtt) cc_final: 0.8163 (ttm)
REVERT: A  218 LYS cc_start: 0.4545 (mtmt) cc_final: 0.4302 (pttt)
REVERT: A  226 HIS cc_start: 0.7146 (t70) cc_final: 0.6778 (t-90)
REVERT: A  244 ASN cc_start: 0.8206 (m-40) cc_final: 0.7830 (t0)
REVERT: A  248 ASN cc_start: 0.7613 (m-40) cc_final: 0.7394 (t0)
REVERT: A  343 TYR cc_start: 0.6439 (t80) cc_final: 0.6216 (t80)
REVERT: A  369 GLU cc_start: 0.8398 (tp30) cc_final: 0.8165 (mm-30)
REVERT: A  370 GLU cc_start: 0.8711 (tt0) cc_final: 0.8411 (tm-30)
REVERT: A  378 ILE cc_start: 0.7865 (mt) cc_final: 0.7592 (mm)
REVERT: A  385 HIS cc_start: 0.5666 (t70) cc_final: 0.5208 (t70)
REVERT: A  464 LEU cc_start: 0.7543 (mt) cc_final: 0.7160 (mt)
REVERT: A  474 SER cc_start: 0.7368 (m) cc_final: 0.6596 (p)
REVERT: B   99 LEU cc_start: 0.6943 (mt) cc_final: 0.6582 (mt)
REVERT: B  290 ARG cc_start: 0.8667 (tpt90) cc_final: 0.8258 (mmm-85)
REVERT: B  344 ARG cc_start: 0.6462 (mmt180) cc_final: 0.6168 (mmm-85)
REVERT: B  363 GLN cc_start: 0.7819 (mp10) cc_final: 0.7457 (tt0)
REVERT: B  435 ILE cc_start: 0.6856 (mt) cc_final: 0.6194 (mt)
REVERT: B  501 ILE cc_start: 0.8156 (mm) cc_final: 0.7781 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2188
  time to fit residues: 73.1453
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.0364

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 375 GLN
B  57 GLN
B 102 GLN
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.189118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.162893 restraints weight = 9121.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.166922 restraints weight = 5318.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.169733 restraints weight = 3540.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6614
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   7084  Z= 0.167
  Angle     :  0.697   8.809   9773  Z= 0.349
  Chirality :  0.042   0.200   1109
  Planarity :  0.006   0.086   1139
  Dihedral  : 17.275 152.314   1470
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.44 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.83 (0.30), residues: 751
  helix:  2.43 (0.30), residues: 286
  sheet:  1.45 (0.56), residues: 86
  loop :  0.27 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 409 
 HIS   0.006   0.001   HIS A 222 
 PHE   0.022   0.002   PHE B 163 
 TYR   0.029   0.003   TYR B  47 
 ARG   0.006   0.001   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05075 (  307)
  hydrogen bonds       : angle       5.62180 (  863)
  covalent geometry    : bond        0.00376 ( 7084)
  covalent geometry    : angle       0.69739 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 180
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.4999 (mtmt) cc_final: 0.4550 (pttt)
REVERT: A  332 GLU cc_start: 0.6689 (pm20) cc_final: 0.6332 (pm20)
REVERT: A  340 ARG cc_start: 0.7505 (mtm110) cc_final: 0.7100 (ptt90)
REVERT: B   78 LYS cc_start: 0.7799 (tptt) cc_final: 0.7063 (mmtp)
REVERT: B  185 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7353 (mp10)
REVERT: B  353 MET cc_start: 0.5888 (mtm) cc_final: 0.5177 (mtm)
REVERT: B  432 ARG cc_start: 0.6877 (mmt180) cc_final: 0.6538 (ttt90)
REVERT: B  438 GLN cc_start: 0.7343 (pt0) cc_final: 0.6910 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2087
  time to fit residues: 49.8621
Evaluate side-chains
  132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 55 optimal weight:    0.5980
   chunk 49 optimal weight:    0.4980
   chunk 20 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:   20.0000
   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 226 HIS
A 363 GLN
B 438 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.186892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.159837 restraints weight = 9286.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163852 restraints weight = 5452.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.166581 restraints weight = 3667.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7084  Z= 0.166
  Angle     :  0.656   9.488   9773  Z= 0.326
  Chirality :  0.041   0.191   1109
  Planarity :  0.005   0.046   1139
  Dihedral  : 16.781 151.421   1470
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: 751
  helix:  2.34 (0.30), residues: 282
  sheet:  0.99 (0.52), residues: 87
  loop :  0.14 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.012   0.001   HIS A 226 
 PHE   0.017   0.002   PHE B 354 
 TYR   0.015   0.002   TYR B  45 
 ARG   0.007   0.001   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 (  307)
  hydrogen bonds       : angle       5.28167 (  863)
  covalent geometry    : bond        0.00377 ( 7084)
  covalent geometry    : angle       0.65593 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 HIS cc_start: 0.6433 (t70) cc_final: 0.5906 (t70)
REVERT: A  428 PHE cc_start: 0.7947 (t80) cc_final: 0.7686 (t80)
REVERT: A  484 TYR cc_start: 0.6812 (m-80) cc_final: 0.6598 (m-10)
REVERT: B   78 LYS cc_start: 0.7952 (tptt) cc_final: 0.7192 (mmtp)
REVERT: B  210 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7448 (tt0)
REVERT: B  274 MET cc_start: 0.6906 (mtt) cc_final: 0.6417 (mtm)
REVERT: B  290 ARG cc_start: 0.8256 (tpt90) cc_final: 0.7929 (mmm-85)
REVERT: B  361 LEU cc_start: 0.8011 (tp) cc_final: 0.7662 (tt)
REVERT: B  432 ARG cc_start: 0.7125 (mmt180) cc_final: 0.6755 (ttm170)
REVERT: B  464 LEU cc_start: 0.7012 (mt) cc_final: 0.6789 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2183
  time to fit residues: 45.3124
Evaluate side-chains
  123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.0670
   chunk 57 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    0.9924

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.186634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159324 restraints weight = 9263.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.163353 restraints weight = 5401.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.166126 restraints weight = 3632.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7084  Z= 0.134
  Angle     :  0.614   7.762   9773  Z= 0.306
  Chirality :  0.040   0.200   1109
  Planarity :  0.005   0.081   1139
  Dihedral  : 16.495 150.664   1470
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.41 (0.30), residues: 751
  helix:  2.29 (0.30), residues: 282
  sheet:  0.64 (0.50), residues: 97
  loop :  0.00 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.017   0.002   PHE B  63 
 TYR   0.018   0.002   TYR B 500 
 ARG   0.007   0.001   ARG B 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  307)
  hydrogen bonds       : angle       4.96136 (  863)
  covalent geometry    : bond        0.00299 ( 7084)
  covalent geometry    : angle       0.61365 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6569 (mmm) cc_final: 0.5989 (mmm)
REVERT: A  274 MET cc_start: 0.3967 (mtp) cc_final: 0.3644 (mtt)
REVERT: A  385 HIS cc_start: 0.6370 (t70) cc_final: 0.5854 (t70)
REVERT: A  410 MET cc_start: 0.4705 (mtt) cc_final: 0.3449 (mtp)
REVERT: A  428 PHE cc_start: 0.8166 (t80) cc_final: 0.7895 (t80)
REVERT: A  431 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7648 (mmt180)
REVERT: A  499 GLN cc_start: 0.6349 (mt0) cc_final: 0.6112 (mt0)
REVERT: B   78 LYS cc_start: 0.8057 (tptt) cc_final: 0.7330 (mmtp)
REVERT: B  274 MET cc_start: 0.7031 (mtt) cc_final: 0.6821 (mtm)
REVERT: B  290 ARG cc_start: 0.8565 (tpt90) cc_final: 0.8150 (mmm-85)
REVERT: B  353 MET cc_start: 0.5927 (mtm) cc_final: 0.5662 (mtm)
REVERT: B  361 LEU cc_start: 0.8260 (tp) cc_final: 0.7872 (tt)
REVERT: B  377 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6775 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2122
  time to fit residues: 43.2777
Evaluate side-chains
  118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    2.2786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.181352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.153458 restraints weight = 9358.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.157257 restraints weight = 5669.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.159855 restraints weight = 3924.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.5464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7084  Z= 0.183
  Angle     :  0.656   7.380   9773  Z= 0.331
  Chirality :  0.042   0.193   1109
  Planarity :  0.005   0.049   1139
  Dihedral  : 16.420 153.136   1470
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.04 (0.30), residues: 751
  helix:  2.08 (0.30), residues: 283
  sheet:  0.14 (0.49), residues: 99
  loop : -0.20 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 409 
 HIS   0.011   0.001   HIS A 226 
 PHE   0.020   0.002   PHE B 371 
 TYR   0.022   0.002   TYR B  45 
 ARG   0.005   0.001   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 (  307)
  hydrogen bonds       : angle       5.14677 (  863)
  covalent geometry    : bond        0.00421 ( 7084)
  covalent geometry    : angle       0.65584 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6801 (mmm) cc_final: 0.6577 (mmm)
REVERT: A  385 HIS cc_start: 0.6490 (t70) cc_final: 0.5999 (t70)
REVERT: A  501 ILE cc_start: 0.6972 (pt) cc_final: 0.6495 (mt)
REVERT: B   78 LYS cc_start: 0.8351 (tptt) cc_final: 0.7568 (mmtp)
REVERT: B  210 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7434 (tt0)
REVERT: B  274 MET cc_start: 0.7325 (mtt) cc_final: 0.6938 (mtm)
REVERT: B  353 MET cc_start: 0.6237 (mtm) cc_final: 0.5912 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2259
  time to fit residues: 47.2841
Evaluate side-chains
  114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 38 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.6384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.179196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.152141 restraints weight = 9363.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.155866 restraints weight = 5654.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.158477 restraints weight = 3871.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.5927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7084  Z= 0.147
  Angle     :  0.619   7.890   9773  Z= 0.313
  Chirality :  0.040   0.167   1109
  Planarity :  0.005   0.047   1139
  Dihedral  : 16.327 153.082   1470
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.01 (0.30), residues: 751
  helix:  2.11 (0.31), residues: 283
  sheet:  0.03 (0.49), residues: 106
  loop : -0.25 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.009   0.001   HIS A 226 
 PHE   0.021   0.002   PHE A 428 
 TYR   0.018   0.002   TYR B  45 
 ARG   0.006   0.001   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03809 (  307)
  hydrogen bonds       : angle       4.85600 (  863)
  covalent geometry    : bond        0.00335 ( 7084)
  covalent geometry    : angle       0.61913 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.5622 (mtmt) cc_final: 0.5018 (mtmt)
REVERT: A  385 HIS cc_start: 0.6372 (t70) cc_final: 0.6039 (t70)
REVERT: A  501 ILE cc_start: 0.7127 (pt) cc_final: 0.6633 (mt)
REVERT: B   78 LYS cc_start: 0.8438 (tptt) cc_final: 0.7642 (mmtp)
REVERT: B  210 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7176 (mm-30)
REVERT: B  274 MET cc_start: 0.7128 (mtt) cc_final: 0.6713 (mtm)
REVERT: B  353 MET cc_start: 0.6231 (mtm) cc_final: 0.5882 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1883
  time to fit residues: 35.8932
Evaluate side-chains
  107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 67 optimal weight:    0.4980
   chunk 62 optimal weight:    6.9990
   chunk 52 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0370
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.182362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.155851 restraints weight = 9277.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.159728 restraints weight = 5510.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.162440 restraints weight = 3727.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.6130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7084  Z= 0.123
  Angle     :  0.608   7.723   9773  Z= 0.303
  Chirality :  0.040   0.200   1109
  Planarity :  0.005   0.045   1139
  Dihedral  : 16.070 151.361   1470
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.11 (0.31), residues: 751
  helix:  2.17 (0.31), residues: 285
  sheet:  0.34 (0.52), residues: 97
  loop : -0.27 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.013   0.001   HIS A 226 
 PHE   0.023   0.002   PHE B 354 
 TYR   0.015   0.001   TYR B  45 
 ARG   0.007   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  307)
  hydrogen bonds       : angle       4.68672 (  863)
  covalent geometry    : bond        0.00273 ( 7084)
  covalent geometry    : angle       0.60777 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.5672 (mtmt) cc_final: 0.5187 (mtmt)
REVERT: A  227 ARG cc_start: 0.6491 (mpp80) cc_final: 0.6283 (mtm180)
REVERT: A  367 LEU cc_start: 0.8842 (tp) cc_final: 0.8639 (tp)
REVERT: A  385 HIS cc_start: 0.6326 (t70) cc_final: 0.5991 (t70)
REVERT: A  499 GLN cc_start: 0.6349 (mt0) cc_final: 0.6092 (mt0)
REVERT: A  501 ILE cc_start: 0.7010 (pt) cc_final: 0.6612 (mt)
REVERT: B   78 LYS cc_start: 0.8318 (tptt) cc_final: 0.7808 (mmtp)
REVERT: B  210 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7038 (mm-30)
REVERT: B  274 MET cc_start: 0.6946 (mtt) cc_final: 0.6581 (mtm)
REVERT: B  353 MET cc_start: 0.6317 (mtm) cc_final: 0.5968 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1817
  time to fit residues: 35.8864
Evaluate side-chains
  115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 77 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   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 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.184725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.157131 restraints weight = 9383.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.160982 restraints weight = 5648.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.163556 restraints weight = 3887.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.6297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7084  Z= 0.126
  Angle     :  0.620   7.721   9773  Z= 0.311
  Chirality :  0.041   0.249   1109
  Planarity :  0.004   0.046   1139
  Dihedral  : 15.903 150.525   1470
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.03 (0.30), residues: 751
  helix:  2.12 (0.31), residues: 284
  sheet: -0.01 (0.48), residues: 109
  loop : -0.23 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.012   0.001   HIS A 226 
 PHE   0.023   0.002   PHE B 354 
 TYR   0.011   0.001   TYR B  45 
 ARG   0.005   0.000   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03468 (  307)
  hydrogen bonds       : angle       4.74722 (  863)
  covalent geometry    : bond        0.00284 ( 7084)
  covalent geometry    : angle       0.61978 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.5525 (mtmt) cc_final: 0.5263 (mtmt)
REVERT: A  385 HIS cc_start: 0.6218 (t70) cc_final: 0.5783 (t70)
REVERT: A  499 GLN cc_start: 0.6042 (mt0) cc_final: 0.5824 (mt0)
REVERT: A  501 ILE cc_start: 0.6985 (pt) cc_final: 0.6677 (mt)
REVERT: B   78 LYS cc_start: 0.8360 (tptt) cc_final: 0.7756 (mmtp)
REVERT: B  143 ARG cc_start: 0.5657 (mmt180) cc_final: 0.5228 (mmt-90)
REVERT: B  210 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7060 (mm-30)
REVERT: B  274 MET cc_start: 0.6936 (mtt) cc_final: 0.6569 (mtm)
REVERT: B  353 MET cc_start: 0.6229 (mtm) cc_final: 0.5949 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1578
  time to fit residues: 30.7435
Evaluate side-chains
  106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 57 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 75 optimal weight:    0.1980
   chunk 9 optimal weight:    0.1980
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 GLN
B 438 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.183420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.155693 restraints weight = 9426.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.159467 restraints weight = 5717.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.162102 restraints weight = 3946.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.6542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7084  Z= 0.130
  Angle     :  0.632   6.969   9773  Z= 0.315
  Chirality :  0.040   0.220   1109
  Planarity :  0.005   0.047   1139
  Dihedral  : 15.751 149.839   1470
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.30), residues: 751
  helix:  2.11 (0.31), residues: 284
  sheet: -0.05 (0.48), residues: 106
  loop : -0.34 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 347 
 PHE   0.024   0.002   PHE B 354 
 TYR   0.021   0.001   TYR B  45 
 ARG   0.008   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  307)
  hydrogen bonds       : angle       4.78822 (  863)
  covalent geometry    : bond        0.00300 ( 7084)
  covalent geometry    : angle       0.63156 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.5503 (mtmt) cc_final: 0.5246 (mtmt)
REVERT: A  293 ASP cc_start: 0.8640 (t0) cc_final: 0.8418 (t70)
REVERT: A  385 HIS cc_start: 0.6021 (t70) cc_final: 0.5638 (t70)
REVERT: A  392 PRO cc_start: 0.7375 (Cg_endo) cc_final: 0.7131 (Cg_exo)
REVERT: A  501 ILE cc_start: 0.6963 (pt) cc_final: 0.6703 (mt)
REVERT: B   78 LYS cc_start: 0.8341 (tptt) cc_final: 0.7735 (mmtp)
REVERT: B  208 ILE cc_start: 0.8181 (mt) cc_final: 0.7437 (mt)
REVERT: B  274 MET cc_start: 0.6915 (mtt) cc_final: 0.6553 (mtm)
REVERT: B  353 MET cc_start: 0.6194 (mtm) cc_final: 0.5927 (mtm)
REVERT: B  376 MET cc_start: 0.7253 (mtp) cc_final: 0.7034 (mtm)
REVERT: B  428 PHE cc_start: 0.7528 (t80) cc_final: 0.7278 (t80)
REVERT: B  436 MET cc_start: 0.7131 (mmt) cc_final: 0.6597 (mmt)
REVERT: B  446 PHE cc_start: 0.7524 (m-80) cc_final: 0.7220 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1558
  time to fit residues: 29.1128
Evaluate side-chains
  102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0270
   chunk 3 optimal weight:    0.0570
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** A 239 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 = 0.4380 r_free = 0.4380 target = 0.185523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.157968 restraints weight = 9478.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.161887 restraints weight = 5668.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.164661 restraints weight = 3864.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.6735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7084  Z= 0.120
  Angle     :  0.616   7.351   9773  Z= 0.307
  Chirality :  0.040   0.241   1109
  Planarity :  0.004   0.046   1139
  Dihedral  : 15.621 148.406   1470
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.30), residues: 751
  helix:  2.09 (0.31), residues: 287
  sheet: -0.18 (0.47), residues: 104
  loop : -0.34 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 409 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.010   0.001   PHE B  63 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.007   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03404 (  307)
  hydrogen bonds       : angle       4.65284 (  863)
  covalent geometry    : bond        0.00273 ( 7084)
  covalent geometry    : angle       0.61562 ( 9773)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  210 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6936 (mt-10)
REVERT: A  216 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6662 (ttt180)
REVERT: A  218 LYS cc_start: 0.5430 (mtmt) cc_final: 0.4822 (pttm)
REVERT: A  293 ASP cc_start: 0.8555 (t0) cc_final: 0.8282 (t70)
REVERT: A  356 VAL cc_start: 0.8608 (t) cc_final: 0.8246 (t)
REVERT: A  367 LEU cc_start: 0.8876 (tp) cc_final: 0.8513 (tp)
REVERT: A  385 HIS cc_start: 0.5861 (t70) cc_final: 0.5481 (t70)
REVERT: A  392 PRO cc_start: 0.7612 (Cg_endo) cc_final: 0.7325 (Cg_exo)
REVERT: A  402 ARG cc_start: 0.6112 (ttm110) cc_final: 0.5792 (tpp80)
REVERT: A  501 ILE cc_start: 0.6954 (pt) cc_final: 0.6676 (mt)
REVERT: B   78 LYS cc_start: 0.8327 (tptt) cc_final: 0.7738 (mmtp)
REVERT: B  208 ILE cc_start: 0.8370 (mt) cc_final: 0.8165 (mt)
REVERT: B  250 LEU cc_start: 0.7929 (mm) cc_final: 0.7720 (mm)
REVERT: B  274 MET cc_start: 0.6941 (mtt) cc_final: 0.6580 (mtm)
REVERT: B  322 MET cc_start: 0.7577 (ptp) cc_final: 0.7229 (ptp)
REVERT: B  376 MET cc_start: 0.7315 (mtp) cc_final: 0.7078 (mtm)
REVERT: B  436 MET cc_start: 0.7151 (mmt) cc_final: 0.6808 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1523
  time to fit residues: 28.4300
Evaluate side-chains
  105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.0470
   chunk 19 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0030
   chunk 70 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0170
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.3526

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 438 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.186747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.159307 restraints weight = 9290.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.163253 restraints weight = 5572.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.166018 restraints weight = 3802.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.6915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7084  Z= 0.114
  Angle     :  0.610  11.709   9773  Z= 0.301
  Chirality :  0.040   0.226   1109
  Planarity :  0.004   0.047   1139
  Dihedral  : 15.388 147.380   1470
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.30), residues: 751
  helix:  2.11 (0.31), residues: 286
  sheet:  0.02 (0.51), residues: 97
  loop : -0.37 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.009   0.001   HIS B 205 
 PHE   0.015   0.001   PHE A 371 
 TYR   0.010   0.001   TYR B  45 
 ARG   0.005   0.000   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03224 (  307)
  hydrogen bonds       : angle       4.62235 (  863)
  covalent geometry    : bond        0.00257 ( 7084)
  covalent geometry    : angle       0.61047 ( 9773)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2310.72 seconds
wall clock time: 40 minutes 56.80 seconds (2456.80 seconds total)