Starting phenix.real_space_refine
on Tue Jul 29 02:55:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p0u_17338/07_2025/8p0u_17338.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p0u_17338/07_2025/8p0u_17338.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p0u_17338/07_2025/8p0u_17338.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p0u_17338/07_2025/8p0u_17338.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p0u_17338/07_2025/8p0u_17338.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p0u_17338/07_2025/8p0u_17338.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    6853      2.51       5
     N    1891      2.21       5
     O    2086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10912
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 5015
          Classifications: {'peptide': 621}
          Link IDs: {'PTRANS': 31, 'TRANS': 589}
    Chain: "B"
      Number of atoms: 4676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4676
          Classifications: {'peptide': 587}
          Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 555}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 833
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 6, 'TRANS': 95}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 123
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 2, 'rna3p': 3}
    Chain: "V"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 264
          Classifications: {'RNA': 12}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 8}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.02, per 1000 atoms: 0.73
  Number of scatterers: 10912
  At special positions: 0
  Unit cell: (101.721, 121.569, 100.894, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P      18     15.00
     Mg      1     11.99
     O    2086      8.00
     N    1891      7.00
     C    6853      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: 2.76
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2486

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      49.9% alpha, 11.4% beta
      2 base pairs and 6 stacking pairs defined.
    Time for finding SS restraints: 3.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 18
      removed outlier: 3.970A  pdb=" N   THR A  18 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 25
    Processing helix  chain 'A' and resid 27 through 47
    Processing helix  chain 'A' and resid 64 through 75
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 128 through 133
    Processing helix  chain 'A' and resid 134 through 155
    Processing helix  chain 'A' and resid 157 through 166
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.563A  pdb=" N   GLN A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.690A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A 280 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
    Processing helix  chain 'A' and resid 305 through 316
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 3.878A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ARG A 345 " --> pdb=" O   MET A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.481A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 400
    Processing helix  chain 'A' and resid 485 through 492
    Processing helix  chain 'A' and resid 493 through 497
    Processing helix  chain 'A' and resid 498 through 517
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.578A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 599
      removed outlier: 3.652A  pdb=" N   LYS A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 617
      removed outlier: 3.524A  pdb=" N   MET A 617 " --> pdb=" O   GLY A 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 5
    Processing helix  chain 'B' and resid 13 through 20
      removed outlier: 3.974A  pdb=" N   GLU B  17 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TYR B  20 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 49
      Proline residue:  B  44  - end of helix
      removed outlier: 4.653A  pdb=" N   TYR B  49 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 58
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 95
    Processing helix  chain 'B' and resid 95 through 109
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 114 through 121
      removed outlier: 3.603A  pdb=" N   GLU B 117 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLY B 121 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 169
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 250 through 266
    Processing helix  chain 'B' and resid 276 through 287
      removed outlier: 4.378A  pdb=" N   LYS B 280 " --> pdb=" O   GLY B 276 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU B 284 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.727A  pdb=" N   CYS B 308 " --> pdb=" O   PHE B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 325
      removed outlier: 3.506A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 344
      Proline residue:  B 338  - end of helix
    Processing helix  chain 'B' and resid 373 through 378
      removed outlier: 4.420A  pdb=" N   ARG B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 407
      removed outlier: 3.717A  pdb=" N   SER B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 451
    Processing helix  chain 'B' and resid 455 through 459
    Processing helix  chain 'B' and resid 496 through 514
    Processing helix  chain 'B' and resid 518 through 537
      removed outlier: 3.591A  pdb=" N   TYR B 537 " --> pdb=" O   TYR B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 552
    Processing helix  chain 'B' and resid 568 through 572
      removed outlier: 4.297A  pdb=" N   MET B 572 " --> pdb=" O   PHE B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 583
    Processing helix  chain 'B' and resid 587 through 595
    Processing helix  chain 'C' and resid 57 through 69
      removed outlier: 5.175A  pdb=" N   VAL C  64 " --> pdb=" O   GLN C  60 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   TYR C  65 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 114
      removed outlier: 4.281A  pdb=" N   ASP C 111 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 142
      removed outlier: 4.681A  pdb=" N   ALA C 131 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   GLU C 132 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS C 135 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 720 through 731
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59
    Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242
      removed outlier: 7.061A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A 475 " --> pdb=" O   MET A 451 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL A 464 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242
      removed outlier: 5.256A  pdb=" N   PHE A 425 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   THR A 416 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY A 427 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.704A  pdb=" N   ARG B 131 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 178
    Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245
      removed outlier: 4.667A  pdb=" N   THR B 228 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS B 345 " --> pdb=" O   CYS B 387 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   CYS B 387 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470
    Processing sheet with id=AB3, first strand: chain 'C' and resid 73 through 75
    Processing sheet with id=AB4, first strand: chain 'C' and resid 84 through 85

    527 hydrogen bonds defined for protein.
    1422 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      5 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      6 stacking parallelities
  Total time for adding SS restraints: 3.61

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3323
        1.33 -     1.45: 1649
        1.45 -     1.57: 6079
        1.57 -     1.69: 34
        1.69 -     1.81: 104
  Bond restraints: 11189
  Sorted by residual:
  bond pdb=" N   SER B 625 "
       pdb=" CA  SER B 625 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.27e-02 6.20e+03 6.71e+00
  bond pdb=" N   TYR B 624 "
       pdb=" CA  TYR B 624 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.14e-02 7.69e+03 6.47e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  bond pdb=" N   ASP B 623 "
       pdb=" CA  ASP B 623 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.28e+00
  bond pdb=" CA  SER B 625 "
       pdb=" CB  SER B 625 "
    ideal  model  delta    sigma   weight residual
    1.529  1.506  0.022 1.66e-02 3.63e+03 1.79e+00
  ... (remaining 11184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.88: 14538
        0.88 -     1.76: 534
        1.76 -     2.64: 85
        2.64 -     3.52: 61
        3.52 -     4.40: 23
  Bond angle restraints: 15241
  Sorted by residual:
  angle pdb=" C   ASN A 524 "
        pdb=" CA  ASN A 524 "
        pdb=" CB  ASN A 524 "
      ideal   model   delta    sigma   weight residual
     111.01  115.41   -4.40 1.38e+00 5.25e-01 1.02e+01
  angle pdb=" CA  SER B 625 "
        pdb=" C   SER B 625 "
        pdb=" O   SER B 625 "
      ideal   model   delta    sigma   weight residual
     121.56  118.16    3.40 1.09e+00 8.42e-01 9.73e+00
  angle pdb=" CA  ASN A 524 "
        pdb=" CB  ASN A 524 "
        pdb=" CG  ASN A 524 "
      ideal   model   delta    sigma   weight residual
     112.60  115.48   -2.88 1.00e+00 1.00e+00 8.29e+00
  angle pdb=" C   TYR B 624 "
        pdb=" N   SER B 625 "
        pdb=" CA  SER B 625 "
      ideal   model   delta    sigma   weight residual
     120.94  124.58   -3.64 1.57e+00 4.06e-01 5.38e+00
  angle pdb=" N   ILE A 494 "
        pdb=" CA  ILE A 494 "
        pdb=" C   ILE A 494 "
      ideal   model   delta    sigma   weight residual
     113.00  110.04    2.96 1.30e+00 5.92e-01 5.18e+00
  ... (remaining 15236 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.88: 6045
       20.88 -    41.75: 552
       41.75 -    62.63: 161
       62.63 -    83.51: 35
       83.51 -   104.38: 8
  Dihedral angle restraints: 6801
    sinusoidal: 2968
      harmonic: 3833
  Sorted by residual:
  dihedral pdb=" CG  ARG B 122 "
           pdb=" CD  ARG B 122 "
           pdb=" NE  ARG B 122 "
           pdb=" CZ  ARG B 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.35   48.65     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CA  ASP B 348 "
           pdb=" CB  ASP B 348 "
           pdb=" CG  ASP B 348 "
           pdb=" OD1 ASP B 348 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.53   58.53     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  ASP B 575 "
           pdb=" CB  ASP B 575 "
           pdb=" CG  ASP B 575 "
           pdb=" OD1 ASP B 575 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.34   57.34     1      2.00e+01 2.50e-03 1.10e+01
  ... (remaining 6798 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1146
       0.030 -    0.059: 399
       0.059 -    0.089: 80
       0.089 -    0.118: 71
       0.118 -    0.148: 13
  Chirality restraints: 1709
  Sorted by residual:
  chirality pdb=" CA  ASN A 524 "
            pdb=" N   ASN A 524 "
            pdb=" C   ASN A 524 "
            pdb=" CB  ASN A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CA  ILE B 385 "
            pdb=" N   ILE B 385 "
            pdb=" C   ILE B 385 "
            pdb=" CB  ILE B 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 192 "
            pdb=" N   ILE A 192 "
            pdb=" C   ILE A 192 "
            pdb=" CB  ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  ... (remaining 1706 not shown)

  Planarity restraints: 1886
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 122 "    0.209 9.50e-02 1.11e+02   9.41e-02 5.98e+00
        pdb=" NE  ARG B 122 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 122 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 122 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 122 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 524 "    0.008 2.00e-02 2.50e+03   1.49e-02 2.21e+00
        pdb=" C   ASN A 524 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ASN A 524 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PRO A 525 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  39 "    0.008 2.00e-02 2.50e+03   8.34e-03 1.39e+00
        pdb=" CG  TYR A  39 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  39 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  39 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  39 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  39 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  39 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1883 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 70
        2.50 -     3.10: 7831
        3.10 -     3.70: 16986
        3.70 -     4.30: 25470
        4.30 -     4.90: 42315
  Nonbonded interactions: 92672
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 423 "
            pdb="MG    MG B 801 "
     model   vdw
     1.895 2.170
  nonbonded pdb=" OG1 THR A 178 "
            pdb=" OE1 GLU B 170 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" OG1 THR A 158 "
            pdb=" OE1 GLU B 100 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" O   ASN A 524 "
            pdb=" OD1 ASN A 524 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG  SER A 268 "
            pdb=" OP1   G V   2 "
     model   vdw
     2.130 3.040
  ... (remaining 92667 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.070
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.090
  Find NCS groups from input model:        0.150
  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:12.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11189  Z= 0.111
  Angle     :  0.455   4.404  15241  Z= 0.239
  Chirality :  0.037   0.148   1709
  Planarity :  0.003   0.094   1886
  Dihedral  : 17.808 104.385   4315
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.47 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.18 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.72 (0.24), residues: 1296
  helix:  1.99 (0.22), residues: 589
  sheet: -0.85 (0.40), residues: 143
  loop : -0.78 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 129 
 PHE   0.009   0.001   PHE A 144 
 TYR   0.020   0.001   TYR A  39 
 ARG   0.013   0.000   ARG B 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13371 (  528)
  hydrogen bonds       : angle       5.16197 ( 1432)
  covalent geometry    : bond        0.00233 (11189)
  covalent geometry    : angle       0.45534 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 1.376 
Fit side-chains
REVERT: C  726 ILE cc_start: 0.8134 (mt) cc_final: 0.7766 (tp)
REVERT: C  728 SER cc_start: 0.8154 (t) cc_final: 0.7864 (p)
  outliers start: 35
  outliers final: 24
  residues processed: 151
  average time/residue: 1.3556
  time to fit residues: 220.7173
Evaluate side-chains
  108 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  412 CYS
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  416 SER
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain C residue  114 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0010
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 524 ASN
A 535 GLN
A 603 ASN
B 129 HIS
B 227 ASN
B 397 ASN
B 429 ASN
B 453 ASN
B 531 HIS
B 582 HIS
C  60 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.067163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.048928 restraints weight = 37355.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 2.80
r_work: 0.2686 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11189  Z= 0.139
  Angle     :  0.540   7.776  15241  Z= 0.276
  Chirality :  0.039   0.141   1709
  Planarity :  0.004   0.035   1886
  Dihedral  : 11.054 105.485   1718
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.01 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.32 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.74 (0.24), residues: 1296
  helix:  1.93 (0.22), residues: 589
  sheet: -0.97 (0.39), residues: 143
  loop : -0.64 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A  13 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.010   0.001   PHE B 145 
 TYR   0.013   0.001   TYR A  39 
 ARG   0.008   0.001   ARG B 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (  528)
  hydrogen bonds       : angle       4.37084 ( 1432)
  covalent geometry    : bond        0.00321 (11189)
  covalent geometry    : angle       0.54000 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 87
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.9005 (pp20)
REVERT: A   32 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8749 (tmt90)
REVERT: A  171 LEU cc_start: 0.8982 (tp) cc_final: 0.8757 (tp)
REVERT: B  304 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8510 (mtpp)
REVERT: C  133 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7927 (t70)
REVERT: C  137 GLN cc_start: 0.8486 (mp10) cc_final: 0.7982 (mp10)
REVERT: C  726 ILE cc_start: 0.8487 (mt) cc_final: 0.8020 (tp)
  outliers start: 38
  outliers final: 10
  residues processed: 118
  average time/residue: 1.3005
  time to fit residues: 166.2816
Evaluate side-chains
  93 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain C residue  133 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 116 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 129 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0060
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
C 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.067159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.048937 restraints weight = 37888.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.82
r_work: 0.2695 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11189  Z= 0.118
  Angle     :  0.505   9.396  15241  Z= 0.251
  Chirality :  0.039   0.134   1709
  Planarity :  0.003   0.033   1886
  Dihedral  : 10.766 104.848   1700
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.08 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.32 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.86 (0.24), residues: 1296
  helix:  1.98 (0.22), residues: 593
  sheet: -0.89 (0.39), residues: 143
  loop : -0.55 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  13 
 HIS   0.007   0.001   HIS B 291 
 PHE   0.011   0.001   PHE B 145 
 TYR   0.012   0.001   TYR B 533 
 ARG   0.006   0.000   ARG B 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  528)
  hydrogen bonds       : angle       4.16729 ( 1432)
  covalent geometry    : bond        0.00267 (11189)
  covalent geometry    : angle       0.50526 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 85
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8386 (tmt90)
REVERT: A  362 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8867 (p)
REVERT: B  304 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8448 (mtpp)
REVERT: C   91 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8610 (mtmm)
REVERT: C  137 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8059 (mp10)
REVERT: C  726 ILE cc_start: 0.8444 (mt) cc_final: 0.8024 (tp)
  outliers start: 36
  outliers final: 9
  residues processed: 112
  average time/residue: 1.2748
  time to fit residues: 154.8351
Evaluate side-chains
  90 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 99 optimal weight:    0.6980
   chunk 79 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0060
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
B 227 ASN
B 531 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.060006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.042084 restraints weight = 38508.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 2.79
r_work: 0.2679 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11189  Z= 0.140
  Angle     :  0.513   9.936  15241  Z= 0.255
  Chirality :  0.039   0.133   1709
  Planarity :  0.003   0.036   1886
  Dihedral  : 10.708 104.260   1696
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.08 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.17 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.95 (0.24), residues: 1296
  helix:  1.98 (0.22), residues: 598
  sheet: -0.78 (0.40), residues: 143
  loop : -0.45 (0.27), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  13 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.013   0.001   TYR B 533 
 ARG   0.006   0.000   ARG C 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03587 (  528)
  hydrogen bonds       : angle       4.12005 ( 1432)
  covalent geometry    : bond        0.00324 (11189)
  covalent geometry    : angle       0.51260 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8576 (tmt90)
REVERT: B  304 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8472 (mtpp)
REVERT: C   91 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8532 (mtmm)
REVERT: C  137 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8103 (mp10)
REVERT: C  726 ILE cc_start: 0.8581 (mt) cc_final: 0.8065 (tp)
  outliers start: 31
  outliers final: 11
  residues processed: 106
  average time/residue: 1.4390
  time to fit residues: 164.9422
Evaluate side-chains
  90 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 95 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 76 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
B 531 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.059454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.041456 restraints weight = 38447.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 2.77
r_work: 0.2659 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11189  Z= 0.169
  Angle     :  0.522   9.729  15241  Z= 0.258
  Chirality :  0.040   0.173   1709
  Planarity :  0.003   0.039   1886
  Dihedral  : 10.709 103.682   1696
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.01 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.00 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.92 (0.24), residues: 1296
  helix:  1.89 (0.22), residues: 598
  sheet: -0.74 (0.40), residues: 143
  loop : -0.38 (0.27), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 230 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.013   0.001   PHE B 145 
 TYR   0.014   0.001   TYR B 533 
 ARG   0.004   0.000   ARG B 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03733 (  528)
  hydrogen bonds       : angle       4.14920 ( 1432)
  covalent geometry    : bond        0.00391 (11189)
  covalent geometry    : angle       0.52161 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 77
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8870 (p)
REVERT: B  304 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8481 (mtpp)
REVERT: C   91 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8534 (mtmm)
REVERT: C  137 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8185 (mp10)
REVERT: C  726 ILE cc_start: 0.8583 (mt) cc_final: 0.8033 (tp)
  outliers start: 32
  outliers final: 15
  residues processed: 101
  average time/residue: 1.3983
  time to fit residues: 152.4906
Evaluate side-chains
  96 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0020
   chunk 36 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.8990

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
B 531 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.059770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.041815 restraints weight = 38413.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 2.77
r_work: 0.2672 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11189  Z= 0.134
  Angle     :  0.502  10.734  15241  Z= 0.250
  Chirality :  0.039   0.193   1709
  Planarity :  0.003   0.037   1886
  Dihedral  : 10.665 103.816   1696
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.01 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.43 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.99 (0.24), residues: 1296
  helix:  1.93 (0.21), residues: 598
  sheet: -0.76 (0.40), residues: 143
  loop : -0.31 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 230 
 HIS   0.007   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.013   0.001   TYR B 533 
 ARG   0.003   0.000   ARG B 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03508 (  528)
  hydrogen bonds       : angle       4.07362 ( 1432)
  covalent geometry    : bond        0.00309 (11189)
  covalent geometry    : angle       0.50157 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8882 (p)
REVERT: B  304 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8482 (mtpp)
REVERT: C   91 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8599 (mtmm)
REVERT: C  137 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (mp10)
REVERT: C  726 ILE cc_start: 0.8616 (mt) cc_final: 0.8065 (tp)
  outliers start: 26
  outliers final: 11
  residues processed: 101
  average time/residue: 1.2966
  time to fit residues: 141.6723
Evaluate side-chains
  88 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 85 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 528 GLN
A 535 GLN
B 227 ASN
B 531 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.059751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.041848 restraints weight = 39064.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 2.77
r_work: 0.2674 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8926
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11189  Z= 0.134
  Angle     :  0.519  12.730  15241  Z= 0.257
  Chirality :  0.039   0.193   1709
  Planarity :  0.003   0.038   1886
  Dihedral  : 10.643 103.754   1696
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.35 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.00 (0.24), residues: 1296
  helix:  1.91 (0.22), residues: 600
  sheet: -0.75 (0.39), residues: 143
  loop : -0.28 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.012   0.001   TYR B 533 
 ARG   0.003   0.000   ARG B 410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03535 (  528)
  hydrogen bonds       : angle       4.07658 ( 1432)
  covalent geometry    : bond        0.00309 (11189)
  covalent geometry    : angle       0.51903 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8919 (p)
REVERT: B  304 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8462 (mtpp)
REVERT: C   91 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8646 (mtmm)
  outliers start: 29
  outliers final: 19
  residues processed: 103
  average time/residue: 1.3065
  time to fit residues: 145.7599
Evaluate side-chains
  98 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  129 LEU
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 104 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0770
   chunk 110 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B 531 HIS
C 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.066467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.048654 restraints weight = 38344.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.74
r_work: 0.2709 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11189  Z= 0.109
  Angle     :  0.505  13.014  15241  Z= 0.251
  Chirality :  0.039   0.195   1709
  Planarity :  0.003   0.038   1886
  Dihedral  : 10.615 103.788   1696
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.52 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.05 (0.24), residues: 1296
  helix:  1.97 (0.22), residues: 599
  sheet: -0.71 (0.40), residues: 143
  loop : -0.27 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 144 
 HIS   0.007   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.011   0.001   TYR B 533 
 ARG   0.003   0.000   ARG B 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03424 (  528)
  hydrogen bonds       : angle       4.03771 ( 1432)
  covalent geometry    : bond        0.00243 (11189)
  covalent geometry    : angle       0.50494 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9021 (p)
REVERT: B  304 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8512 (mtpp)
REVERT: B  332 MET cc_start: 0.8870 (mmm) cc_final: 0.8360 (mtt)
REVERT: C   91 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8583 (mtmm)
  outliers start: 26
  outliers final: 17
  residues processed: 99
  average time/residue: 1.3537
  time to fit residues: 145.0083
Evaluate side-chains
  95 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  129 LEU
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 128 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 107 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 126 optimal weight:    0.0570
   chunk 2 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
A 604 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.060049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.042342 restraints weight = 39225.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 2.77
r_work: 0.2705 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11189  Z= 0.117
  Angle     :  0.521  13.171  15241  Z= 0.255
  Chirality :  0.039   0.202   1709
  Planarity :  0.003   0.038   1886
  Dihedral  : 10.575 103.379   1696
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 22.95 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.12 (0.24), residues: 1296
  helix:  1.99 (0.22), residues: 599
  sheet: -0.65 (0.40), residues: 143
  loop : -0.21 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 144 
 HIS   0.007   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.012   0.001   TYR B 533 
 ARG   0.003   0.000   ARG B 410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  528)
  hydrogen bonds       : angle       4.03093 ( 1432)
  covalent geometry    : bond        0.00267 (11189)
  covalent geometry    : angle       0.52139 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9038 (p)
REVERT: B  248 MET cc_start: 0.9045 (mmt) cc_final: 0.8799 (mmt)
REVERT: B  304 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8469 (mtpp)
REVERT: C   91 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8593 (mtmm)
  outliers start: 23
  outliers final: 17
  residues processed: 96
  average time/residue: 1.3487
  time to fit residues: 140.2792
Evaluate side-chains
  95 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  304 LYS
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  129 LEU
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0670
   chunk 109 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0570
   chunk 14 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 108 optimal weight:    0.1980
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
A 528 GLN
A 573 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.060559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.043334 restraints weight = 39136.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.68
r_work: 0.2733 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11189  Z= 0.101
  Angle     :  0.521  13.402  15241  Z= 0.254
  Chirality :  0.039   0.202   1709
  Planarity :  0.003   0.038   1886
  Dihedral  : 10.513 102.994   1696
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 23.37 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.15 (0.24), residues: 1296
  helix:  2.01 (0.22), residues: 599
  sheet: -0.59 (0.40), residues: 143
  loop : -0.18 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 614 
 HIS   0.007   0.001   HIS B 291 
 PHE   0.011   0.001   PHE B 145 
 TYR   0.011   0.001   TYR B 533 
 ARG   0.005   0.000   ARG C 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03219 (  528)
  hydrogen bonds       : angle       3.98095 ( 1432)
  covalent geometry    : bond        0.00226 (11189)
  covalent geometry    : angle       0.52115 (15241)

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9072 (p)
REVERT: C   91 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8581 (mtmm)
  outliers start: 20
  outliers final: 17
  residues processed: 96
  average time/residue: 1.3914
  time to fit residues: 144.3694
Evaluate side-chains
  97 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  200 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  475 HIS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   91 LYS
Chi-restraints excluded: chain C residue  129 LEU
Chi-restraints excluded: chain C residue  137 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0870
   chunk 84 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.060255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.042640 restraints weight = 38608.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.72
r_work: 0.2718 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11189  Z= 0.117
  Angle     :  0.531  13.332  15241  Z= 0.257
  Chirality :  0.039   0.209   1709
  Planarity :  0.003   0.038   1886
  Dihedral  : 10.478 102.541   1696
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 23.80 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  1.20 (0.24), residues: 1296
  helix:  2.03 (0.22), residues: 598
  sheet: -0.52 (0.40), residues: 143
  loop : -0.15 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.007   0.001   HIS B 291 
 PHE   0.012   0.001   PHE B 145 
 TYR   0.011   0.001   TYR B 533 
 ARG   0.006   0.000   ARG C 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  528)
  hydrogen bonds       : angle       4.00135 ( 1432)
  covalent geometry    : bond        0.00267 (11189)
  covalent geometry    : angle       0.53128 (15241)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6340.92 seconds
wall clock time: 110 minutes 24.53 seconds (6624.53 seconds total)