Starting phenix.real_space_refine
on Fri Feb 14 15:23:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sh3_40479/02_2025/8sh3_40479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sh3_40479/02_2025/8sh3_40479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sh3_40479/02_2025/8sh3_40479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sh3_40479/02_2025/8sh3_40479.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sh3_40479/02_2025/8sh3_40479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sh3_40479/02_2025/8sh3_40479.cif"
  }
  resolution = 2.8
  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=  -0.002 sd=   0.100
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
     I       4     10.91       5
     P       6      5.49       5
     S      36      5.16       5
     C    7004      2.51       5
     N    1542      2.21       5
     O    1794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10386
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 4755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4755
          Classifications: {'peptide': 613}
          Link IDs: {'PTRANS': 24, 'TRANS': 588}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 4755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4755
          Classifications: {'peptide': 613}
          Link IDs: {'PTRANS': 24, 'TRANS': 588}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 438
          Unusual residues: {'AV0': 2, 'CLR': 6, 'IOD': 2, 'LBN': 9}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          Unresolved non-hydrogen bonds: 340
          Unresolved non-hydrogen angles: 420
          Unresolved non-hydrogen dihedrals: 351
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7}
          Unresolved non-hydrogen planarities: 72
    Chain: "D"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 438
          Unusual residues: {'AV0': 2, 'CLR': 6, 'IOD': 2, 'LBN': 9}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          Unresolved non-hydrogen bonds: 340
          Unresolved non-hydrogen angles: 420
          Unresolved non-hydrogen dihedrals: 351
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7}
          Unresolved non-hydrogen planarities: 72
  Time building chain proxies: 7.09, per 1000 atoms: 0.68
  Number of scatterers: 10386
  At special positions: 0
  Unit cell: (85.078, 121.422, 105.728, 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)
     I       4     52.95
     S      36     16.00
     P       6     15.00
     O    1794      8.00
     N    1542      7.00
     C    7004      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 5 sheets defined
      70.2% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'C' and resid 28 through 36
    Processing helix  chain 'C' and resid 70 through 74
    Processing helix  chain 'C' and resid 82 through 109
      removed outlier: 4.050A  pdb=" N   SER C  86 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU C 100 " --> pdb=" O   LEU C  96 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU C 107 " --> pdb=" O   MET C 103 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU C 108 " --> pdb=" O   ALA C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 131
      removed outlier: 3.596A  pdb=" N   TYR C 118 " --> pdb=" O   GLY C 114 " (cutoff:3.500A)
      Proline residue:  C 123  - end of helix
      removed outlier: 4.188A  pdb=" N   ILE C 129 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   PHE C 130 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 156
      removed outlier: 3.522A  pdb=" N   SER C 145 " --> pdb=" O   PHE C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 162
    Processing helix  chain 'C' and resid 177 through 206
    Processing helix  chain 'C' and resid 210 through 215
      removed outlier: 3.852A  pdb=" N   TYR C 214 " --> pdb=" O   PHE C 210 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU C 215 " --> pdb=" O   ILE C 211 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 210 through 215'
    Processing helix  chain 'C' and resid 216 through 241
    Processing helix  chain 'C' and resid 251 through 264
    Processing helix  chain 'C' and resid 265 through 267
      No H-bonds generated for 'chain 'C' and resid 265 through 267'
    Processing helix  chain 'C' and resid 268 through 292
    Processing helix  chain 'C' and resid 301 through 318
    Processing helix  chain 'C' and resid 318 through 323
    Processing helix  chain 'C' and resid 342 through 348
      removed outlier: 4.053A  pdb=" N   SER C 347 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 376
      removed outlier: 3.593A  pdb=" N   LYS C 374 " --> pdb=" O   VAL C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 398
    Processing helix  chain 'C' and resid 406 through 416
    Processing helix  chain 'C' and resid 421 through 437
    Processing helix  chain 'C' and resid 446 through 458
      removed outlier: 3.901A  pdb=" N   LEU C 450 " --> pdb=" O   GLN C 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 463
    Processing helix  chain 'C' and resid 466 through 475
      removed outlier: 4.502A  pdb=" N   ARG C 470 " --> pdb=" O   CYS C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 475 through 491
    Processing helix  chain 'C' and resid 493 through 515
    Processing helix  chain 'C' and resid 533 through 537
      removed outlier: 4.194A  pdb=" N   LYS C 537 " --> pdb=" O   THR C 533 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 533 through 537'
    Processing helix  chain 'C' and resid 555 through 571
    Processing helix  chain 'C' and resid 573 through 585
    Processing helix  chain 'C' and resid 669 through 685
    Processing helix  chain 'C' and resid 696 through 706
    Processing helix  chain 'C' and resid 723 through 731
    Processing helix  chain 'D' and resid 28 through 36
    Processing helix  chain 'D' and resid 70 through 74
    Processing helix  chain 'D' and resid 82 through 109
      removed outlier: 4.144A  pdb=" N   SER D  86 " --> pdb=" O   GLU D  82 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU D 100 " --> pdb=" O   LEU D  96 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU D 107 " --> pdb=" O   MET D 103 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 114 through 131
      removed outlier: 3.585A  pdb=" N   TYR D 118 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
      Proline residue:  D 123  - end of helix
      removed outlier: 4.227A  pdb=" N   ILE D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   PHE D 130 " --> pdb=" O   THR D 126 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 156
      removed outlier: 3.521A  pdb=" N   SER D 145 " --> pdb=" O   PHE D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 162
    Processing helix  chain 'D' and resid 177 through 207
    Processing helix  chain 'D' and resid 210 through 215
      removed outlier: 3.866A  pdb=" N   TYR D 214 " --> pdb=" O   PHE D 210 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU D 215 " --> pdb=" O   ILE D 211 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 210 through 215'
    Processing helix  chain 'D' and resid 216 through 241
    Processing helix  chain 'D' and resid 251 through 264
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 268 through 292
    Processing helix  chain 'D' and resid 301 through 318
    Processing helix  chain 'D' and resid 342 through 348
      removed outlier: 4.067A  pdb=" N   SER D 347 " --> pdb=" O   SER D 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 349 through 376
      removed outlier: 3.652A  pdb=" N   SER D 355 " --> pdb=" O   THR D 351 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS D 374 " --> pdb=" O   VAL D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 398
    Processing helix  chain 'D' and resid 406 through 416
    Processing helix  chain 'D' and resid 421 through 437
    Processing helix  chain 'D' and resid 446 through 458
      removed outlier: 3.867A  pdb=" N   LEU D 450 " --> pdb=" O   GLN D 446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 458 through 463
    Processing helix  chain 'D' and resid 466 through 475
      removed outlier: 4.305A  pdb=" N   ARG D 470 " --> pdb=" O   CYS D 466 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 475 through 491
    Processing helix  chain 'D' and resid 493 through 515
    Processing helix  chain 'D' and resid 533 through 537
      removed outlier: 4.197A  pdb=" N   LYS D 537 " --> pdb=" O   THR D 533 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 533 through 537'
    Processing helix  chain 'D' and resid 555 through 571
    Processing helix  chain 'D' and resid 573 through 585
    Processing helix  chain 'D' and resid 669 through 685
    Processing helix  chain 'D' and resid 696 through 706
    Processing helix  chain 'D' and resid 723 through 731
    Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 25
    Processing sheet with id=AA2, first strand: chain 'C' and resid 138 through 139
    Processing sheet with id=AA3, first strand: chain 'C' and resid 530 through 532
      removed outlier: 4.273A  pdb=" N   ILE C 547 " --> pdb=" O   LEU C 521 " (cutoff:3.500A)
      removed outlier: 8.768A  pdb=" N   SER C 523 " --> pdb=" O   VAL C 545 " (cutoff:3.500A)
      removed outlier: 12.667A  pdb=" N   VAL C 545 " --> pdb=" O   SER C 523 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LYS C 546 " --> pdb=" O   VAL C 659 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   ASP C 661 " --> pdb=" O   LYS C 546 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU C 548 " --> pdb=" O   ASP C 661 " (cutoff:3.500A)
      removed outlier: 8.322A  pdb=" N   PHE C 719 " --> pdb=" O   VAL C 690 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE C 692 " --> pdb=" O   PHE C 719 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 138 through 139
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
      removed outlier: 4.269A  pdb=" N   ILE D 547 " --> pdb=" O   LEU D 521 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   SER D 523 " --> pdb=" O   VAL D 545 " (cutoff:3.500A)
      removed outlier: 12.668A  pdb=" N   VAL D 545 " --> pdb=" O   SER D 523 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE D 550 " --> pdb=" O   ASP D 661 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   PHE D 719 " --> pdb=" O   VAL D 690 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   PHE D 692 " --> pdb=" O   PHE D 719 " (cutoff:3.500A)

    626 hydrogen bonds defined for protein.
    1842 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.02

  Time building geometry restraints manager: 3.31 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1531
        1.32 -     1.44: 2634
        1.44 -     1.57: 6373
        1.57 -     1.69: 12
        1.69 -     1.81: 56
  Bond restraints: 10606
  Sorted by residual:
  bond pdb=" O2  LBN C 813 "
       pdb=" P1  LBN C 813 "
    ideal  model  delta    sigma   weight residual
    1.650  1.596  0.054 2.00e-02 2.50e+03 7.36e+00
  bond pdb=" O2  LBN D 813 "
       pdb=" P1  LBN D 813 "
    ideal  model  delta    sigma   weight residual
    1.650  1.596  0.054 2.00e-02 2.50e+03 7.34e+00
  bond pdb=" O2  LBN C 811 "
       pdb=" P1  LBN C 811 "
    ideal  model  delta    sigma   weight residual
    1.650  1.596  0.054 2.00e-02 2.50e+03 7.34e+00
  bond pdb=" O2  LBN C 810 "
       pdb=" P1  LBN C 810 "
    ideal  model  delta    sigma   weight residual
    1.650  1.596  0.054 2.00e-02 2.50e+03 7.34e+00
  bond pdb=" O2  LBN D 810 "
       pdb=" P1  LBN D 810 "
    ideal  model  delta    sigma   weight residual
    1.650  1.596  0.054 2.00e-02 2.50e+03 7.25e+00
  ... (remaining 10601 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 14138
        2.20 -     4.40: 220
        4.40 -     6.60: 16
        6.60 -     8.80: 2
        8.80 -    11.00: 6
  Bond angle restraints: 14382
  Sorted by residual:
  angle pdb=" O1  LBN D 813 "
        pdb=" P1  LBN D 813 "
        pdb=" O2  LBN D 813 "
      ideal   model   delta    sigma   weight residual
      93.45  104.45  -11.00 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" O1  LBN D 810 "
        pdb=" P1  LBN D 810 "
        pdb=" O2  LBN D 810 "
      ideal   model   delta    sigma   weight residual
      93.45  104.17  -10.72 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" O1  LBN C 810 "
        pdb=" P1  LBN C 810 "
        pdb=" O2  LBN C 810 "
      ideal   model   delta    sigma   weight residual
      93.45  104.14  -10.69 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" O1  LBN C 813 "
        pdb=" P1  LBN C 813 "
        pdb=" O2  LBN C 813 "
      ideal   model   delta    sigma   weight residual
      93.45  104.04  -10.59 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" O1  LBN D 811 "
        pdb=" P1  LBN D 811 "
        pdb=" O2  LBN D 811 "
      ideal   model   delta    sigma   weight residual
      93.45  103.76  -10.31 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 14377 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.53: 6833
       34.53 -    69.07: 207
       69.07 -   103.60: 45
      103.60 -   138.14: 56
      138.14 -   172.67: 9
  Dihedral angle restraints: 7150
    sinusoidal: 3600
      harmonic: 3550
  Sorted by residual:
  dihedral pdb=" CA  VAL C 722 "
           pdb=" C   VAL C 722 "
           pdb=" N   HIS C 723 "
           pdb=" CA  HIS C 723 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.87   28.13     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  VAL D 722 "
           pdb=" C   VAL D 722 "
           pdb=" N   HIS D 723 "
           pdb=" CA  HIS D 723 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.87   28.13     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" C1  LBN D 810 "
           pdb=" O1  LBN D 810 "
           pdb=" P1  LBN D 810 "
           pdb=" O3  LBN D 810 "
      ideal   model   delta sinusoidal    sigma   weight residual
     275.40  102.73  172.67     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 7147 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.971: 1756
       0.971 -    1.943: 0
       1.943 -    2.914: 0
       2.914 -    3.885: 0
       3.885 -    4.856: 2
  Chirality restraints: 1758
  Sorted by residual:
  chirality pdb=" C2  LBN C 813 "
            pdb=" C1  LBN C 813 "
            pdb=" C3  LBN C 813 "
            pdb=" O7  LBN C 813 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.49   -4.86 2.00e-01 2.50e+01 5.90e+02
  chirality pdb=" C2  LBN D 813 "
            pdb=" C1  LBN D 813 "
            pdb=" C3  LBN D 813 "
            pdb=" O7  LBN D 813 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.46   -4.83 2.00e-01 2.50e+01 5.82e+02
  chirality pdb=" C2  LBN D 811 "
            pdb=" C1  LBN D 811 "
            pdb=" C3  LBN D 811 "
            pdb=" O7  LBN D 811 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.60    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1755 not shown)

  Planarity restraints: 1638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN C 813 "   -0.100 2.00e-02 2.50e+03   2.28e-01 5.20e+02
        pdb=" C42 LBN C 813 "    0.307 2.00e-02 2.50e+03
        pdb=" C5  LBN C 813 "   -0.307 2.00e-02 2.50e+03
        pdb=" C8  LBN C 813 "    0.100 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN D 813 "    0.217 2.00e-02 2.50e+03   2.17e-01 4.72e+02
        pdb=" C42 LBN D 813 "   -0.215 2.00e-02 2.50e+03
        pdb=" C5  LBN D 813 "   -0.219 2.00e-02 2.50e+03
        pdb=" C8  LBN D 813 "    0.218 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 LBN C 810 "    0.095 2.00e-02 2.50e+03   2.09e-01 4.35e+02
        pdb=" C42 LBN C 810 "   -0.279 2.00e-02 2.50e+03
        pdb=" C5  LBN C 810 "    0.279 2.00e-02 2.50e+03
        pdb=" C8  LBN C 810 "   -0.095 2.00e-02 2.50e+03
  ... (remaining 1635 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 813
        2.74 -     3.30: 11017
        3.30 -     3.85: 18599
        3.85 -     4.41: 23383
        4.41 -     4.96: 38834
  Nonbonded interactions: 92646
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  78 "
            pdb=" OD2 ASP D  87 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   PRO C 553 "
            pdb=" ND2 ASN C 558 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   PRO D 553 "
            pdb=" ND2 ASN D 558 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OH  TYR C  78 "
            pdb=" OD2 ASP C  87 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OH  TYR C 247 "
            pdb=" OE1 GLU C 259 "
     model   vdw
     2.276 3.040
  ... (remaining 92641 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             1.340
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.860
  Find NCS groups from input model:        0.470
  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:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
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      :  0.004   0.054  10606  Z= 0.260
  Angle     :  0.651  11.001  14382  Z= 0.310
  Chirality :  0.169   4.856   1758
  Planarity :  0.011   0.228   1638
  Dihedral  : 21.604 172.671   4862
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.02 (0.25), residues: 1210
  helix:  1.74 (0.19), residues: 802
  sheet:  1.57 (0.77), residues: 36
  loop : -1.88 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 482 
 HIS   0.002   0.001   HIS D 656 
 PHE   0.017   0.001   PHE D 141 
 TYR   0.012   0.001   TYR C 371 
 ARG   0.002   0.000   ARG D 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.052 
Fit side-chains
REVERT: C   79 ARG cc_start: 0.6657 (mmm-85) cc_final: 0.6188 (mtp180)
REVERT: C  440 LYS cc_start: 0.7426 (ttmm) cc_final: 0.6726 (mptt)
REVERT: D   35 GLN cc_start: 0.7316 (tt0) cc_final: 0.7094 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.9920
  time to fit residues: 144.0659
Evaluate side-chains
  106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
D 241 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.173231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.138897 restraints weight = 6899.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 1.37
r_work: 0.3536 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10606  Z= 0.280
  Angle     :  0.699  11.112  14382  Z= 0.339
  Chirality :  0.047   0.205   1758
  Planarity :  0.005   0.076   1638
  Dihedral  : 19.504 178.167   2714
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.79 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.74 %
    Favored  : 90.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.77 (0.24), residues: 1210
  helix:  1.36 (0.18), residues: 838
  sheet:  1.48 (0.73), residues: 34
  loop : -1.79 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  74 
 HIS   0.003   0.001   HIS C 698 
 PHE   0.021   0.002   PHE D 141 
 TYR   0.016   0.002   TYR D 371 
 ARG   0.004   0.000   ARG C  24 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.993 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7669 (tt0) cc_final: 0.7202 (tm-30)
REVERT: C   79 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.6110 (mtp180)
REVERT: C  307 THR cc_start: 0.8259 (m) cc_final: 0.8023 (p)
REVERT: C  438 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8121 (mm)
REVERT: C  440 LYS cc_start: 0.7404 (ttmm) cc_final: 0.6649 (mptt)
REVERT: D   35 GLN cc_start: 0.7653 (tt0) cc_final: 0.7205 (tm-30)
REVERT: D   38 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7097 (ttt180)
REVERT: D  307 THR cc_start: 0.8215 (m) cc_final: 0.7962 (p)
REVERT: D  322 ASN cc_start: 0.7781 (m110) cc_final: 0.7487 (m110)
REVERT: D  438 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8065 (mm)
REVERT: D  440 LYS cc_start: 0.7293 (ttmm) cc_final: 0.6544 (mptt)
  outliers start: 17
  outliers final: 7
  residues processed: 133
  average time/residue: 1.0004
  time to fit residues: 146.4020
Evaluate side-chains
  119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  721 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0370
   chunk 76 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
C 263 ASN
D 241 ASN
D 263 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.176052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142057 restraints weight = 7559.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.44
r_work: 0.3572 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10606  Z= 0.176
  Angle     :  0.597   8.010  14382  Z= 0.296
  Chirality :  0.045   0.272   1758
  Planarity :  0.005   0.081   1638
  Dihedral  : 17.407 173.694   2714
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.63 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  8.89 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: 1210
  helix:  1.61 (0.18), residues: 828
  sheet:  1.11 (0.70), residues: 34
  loop : -1.62 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 482 
 HIS   0.002   0.001   HIS D 728 
 PHE   0.016   0.001   PHE C 141 
 TYR   0.013   0.001   TYR C 371 
 ARG   0.002   0.000   ARG C 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 1.051 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7540 (tt0) cc_final: 0.7052 (tm-30)
REVERT: C   79 ARG cc_start: 0.6603 (mmm-85) cc_final: 0.6043 (mtp180)
REVERT: C  307 THR cc_start: 0.8014 (m) cc_final: 0.7752 (p)
REVERT: C  440 LYS cc_start: 0.7342 (ttmm) cc_final: 0.6559 (mptt)
REVERT: C  655 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7185 (mp)
REVERT: D   35 GLN cc_start: 0.7543 (tt0) cc_final: 0.7109 (tm-30)
REVERT: D   38 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7000 (ttt180)
REVERT: D  307 THR cc_start: 0.7992 (m) cc_final: 0.7745 (p)
REVERT: D  322 ASN cc_start: 0.7731 (m110) cc_final: 0.7371 (m110)
REVERT: D  440 LYS cc_start: 0.7153 (ttmm) cc_final: 0.6377 (mptt)
REVERT: D  689 HIS cc_start: 0.8296 (m-70) cc_final: 0.8071 (m90)
  outliers start: 22
  outliers final: 8
  residues processed: 131
  average time/residue: 1.0066
  time to fit residues: 144.7404
Evaluate side-chains
  123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  288 LEU
Chi-restraints excluded: chain D residue  545 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 109 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.175945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.141252 restraints weight = 7670.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.47
r_work: 0.3578 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10606  Z= 0.184
  Angle     :  0.600   7.715  14382  Z= 0.295
  Chirality :  0.046   0.354   1758
  Planarity :  0.005   0.081   1638
  Dihedral  : 15.954 164.393   2714
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.12 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  9.56 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.18 (0.25), residues: 1210
  helix:  1.70 (0.18), residues: 826
  sheet:  1.08 (0.70), residues: 34
  loop : -1.52 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  74 
 HIS   0.002   0.001   HIS D 656 
 PHE   0.017   0.001   PHE C 141 
 TYR   0.013   0.001   TYR C 323 
 ARG   0.002   0.000   ARG D 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 1.138 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7577 (tt0) cc_final: 0.7117 (tm-30)
REVERT: C  307 THR cc_start: 0.8079 (m) cc_final: 0.7806 (p)
REVERT: C  440 LYS cc_start: 0.7367 (ttmm) cc_final: 0.6610 (mptt)
REVERT: C  655 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7130 (mp)
REVERT: D   35 GLN cc_start: 0.7596 (tt0) cc_final: 0.7172 (tm-30)
REVERT: D   38 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7087 (ttt180)
REVERT: D  307 THR cc_start: 0.8022 (m) cc_final: 0.7761 (p)
REVERT: D  318 ASN cc_start: 0.7405 (t0) cc_final: 0.6944 (t0)
REVERT: D  322 ASN cc_start: 0.7735 (m110) cc_final: 0.7421 (m110)
REVERT: D  385 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7692 (m-80)
REVERT: D  440 LYS cc_start: 0.7192 (ttmm) cc_final: 0.6425 (mptt)
  outliers start: 26
  outliers final: 7
  residues processed: 145
  average time/residue: 0.9882
  time to fit residues: 157.9213
Evaluate side-chains
  127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0670
   chunk 76 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 113 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0770
   chunk 115 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
D 241 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.177528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.143288 restraints weight = 7591.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.46
r_work: 0.3597 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10606  Z= 0.166
  Angle     :  0.583   7.894  14382  Z= 0.289
  Chirality :  0.046   0.353   1758
  Planarity :  0.005   0.079   1638
  Dihedral  : 14.888 155.042   2714
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.85 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.26 (0.25), residues: 1210
  helix:  1.76 (0.18), residues: 826
  sheet:  1.16 (0.71), residues: 34
  loop : -1.49 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 482 
 HIS   0.002   0.001   HIS D 656 
 PHE   0.016   0.001   PHE C 141 
 TYR   0.015   0.001   TYR C 323 
 ARG   0.002   0.000   ARG D 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 1.127 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7521 (tt0) cc_final: 0.7070 (tm-30)
REVERT: C  307 THR cc_start: 0.7975 (m) cc_final: 0.7705 (p)
REVERT: C  440 LYS cc_start: 0.7312 (ttmm) cc_final: 0.6533 (mptt)
REVERT: C  655 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7001 (mp)
REVERT: D   35 GLN cc_start: 0.7532 (tt0) cc_final: 0.7114 (tm-30)
REVERT: D  307 THR cc_start: 0.7965 (m) cc_final: 0.7704 (p)
REVERT: D  318 ASN cc_start: 0.7319 (t0) cc_final: 0.6765 (t0)
REVERT: D  322 ASN cc_start: 0.7761 (m110) cc_final: 0.7416 (m110)
REVERT: D  385 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7425 (m-80)
REVERT: D  440 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6366 (mptt)
  outliers start: 18
  outliers final: 10
  residues processed: 137
  average time/residue: 1.0287
  time to fit residues: 154.3622
Evaluate side-chains
  127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  545 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 109 optimal weight:    0.0170
   chunk 29 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.176215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.141731 restraints weight = 7522.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.46
r_work: 0.3577 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  10606  Z= 0.185
  Angle     :  0.590   9.392  14382  Z= 0.295
  Chirality :  0.046   0.339   1758
  Planarity :  0.005   0.080   1638
  Dihedral  : 14.373 146.949   2714
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.88 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.24 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.18 (0.24), residues: 1210
  helix:  1.69 (0.18), residues: 826
  sheet:  1.25 (0.69), residues: 34
  loop : -1.50 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  83 
 HIS   0.002   0.001   HIS D 656 
 PHE   0.016   0.001   PHE D 141 
 TYR   0.015   0.001   TYR C 323 
 ARG   0.002   0.000   ARG D  38 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 1.089 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7556 (tt0) cc_final: 0.7100 (tm-30)
REVERT: C   79 ARG cc_start: 0.6823 (mmm160) cc_final: 0.5956 (mtp180)
REVERT: C  307 THR cc_start: 0.8030 (m) cc_final: 0.7730 (p)
REVERT: C  318 ASN cc_start: 0.7368 (t0) cc_final: 0.6795 (t0)
REVERT: C  322 ASN cc_start: 0.7734 (m-40) cc_final: 0.7397 (m110)
REVERT: C  385 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7591 (m-80)
REVERT: C  440 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6551 (mptt)
REVERT: C  655 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6919 (mp)
REVERT: D   35 GLN cc_start: 0.7586 (tt0) cc_final: 0.7238 (tm-30)
REVERT: D  307 THR cc_start: 0.8000 (m) cc_final: 0.7732 (p)
REVERT: D  318 ASN cc_start: 0.7307 (t0) cc_final: 0.6737 (t0)
REVERT: D  322 ASN cc_start: 0.7769 (m110) cc_final: 0.7394 (m110)
REVERT: D  385 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7429 (m-80)
REVERT: D  440 LYS cc_start: 0.7149 (ttmm) cc_final: 0.6377 (mptt)
  outliers start: 21
  outliers final: 12
  residues processed: 136
  average time/residue: 0.9889
  time to fit residues: 148.0783
Evaluate side-chains
  133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain C residue  385 PHE
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  721 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0050
   chunk 94 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0070
   overall best weight:    0.4612

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

Flipped N/Q/H residues before XYZ refinement:
C 289 ASN
D 241 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.178131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.144241 restraints weight = 7513.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 1.45
r_work: 0.3606 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10606  Z= 0.163
  Angle     :  0.561   8.942  14382  Z= 0.284
  Chirality :  0.044   0.278   1758
  Planarity :  0.005   0.077   1638
  Dihedral  : 13.654 143.124   2714
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.48 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.33 (0.24), residues: 1210
  helix:  1.81 (0.18), residues: 814
  sheet:  1.25 (0.69), residues: 34
  loop : -1.35 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 482 
 HIS   0.002   0.001   HIS D 728 
 PHE   0.016   0.001   PHE D 141 
 TYR   0.013   0.001   TYR C 323 
 ARG   0.005   0.000   ARG C 576 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 1.064 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7624 (tt0) cc_final: 0.7171 (tm-30)
REVERT: C   79 ARG cc_start: 0.6905 (mmm160) cc_final: 0.6014 (mtp180)
REVERT: C  307 THR cc_start: 0.8047 (m) cc_final: 0.7794 (p)
REVERT: C  318 ASN cc_start: 0.7371 (t0) cc_final: 0.6824 (t0)
REVERT: C  322 ASN cc_start: 0.7763 (m-40) cc_final: 0.7454 (m110)
REVERT: C  385 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7590 (m-80)
REVERT: C  440 LYS cc_start: 0.7344 (ttmm) cc_final: 0.6586 (mptt)
REVERT: C  655 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6975 (mp)
REVERT: D   35 GLN cc_start: 0.7581 (tt0) cc_final: 0.7259 (tm-30)
REVERT: D  318 ASN cc_start: 0.7394 (t0) cc_final: 0.6841 (t0)
REVERT: D  322 ASN cc_start: 0.7791 (m110) cc_final: 0.7431 (m110)
REVERT: D  385 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7339 (m-80)
REVERT: D  440 LYS cc_start: 0.7166 (ttmm) cc_final: 0.6412 (mptt)
  outliers start: 20
  outliers final: 11
  residues processed: 142
  average time/residue: 0.9498
  time to fit residues: 149.2872
Evaluate side-chains
  127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain C residue  385 PHE
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  545 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0170
   chunk 69 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 102 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.176470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.142191 restraints weight = 7693.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.47
r_work: 0.3582 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10606  Z= 0.181
  Angle     :  0.572   9.660  14382  Z= 0.290
  Chirality :  0.044   0.241   1758
  Planarity :  0.005   0.080   1638
  Dihedral  : 13.295 140.283   2714
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.88 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.38 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.30 (0.24), residues: 1210
  helix:  1.78 (0.18), residues: 814
  sheet:  1.23 (0.68), residues: 34
  loop : -1.35 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 482 
 HIS   0.002   0.001   HIS D 728 
 PHE   0.016   0.001   PHE D 141 
 TYR   0.015   0.001   TYR C 105 
 ARG   0.002   0.000   ARG D 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 1.105 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7682 (tt0) cc_final: 0.7322 (tm-30)
REVERT: C   79 ARG cc_start: 0.6960 (mmm160) cc_final: 0.6100 (mtp180)
REVERT: C  307 THR cc_start: 0.8176 (m) cc_final: 0.7909 (p)
REVERT: C  318 ASN cc_start: 0.7475 (t0) cc_final: 0.7173 (t0)
REVERT: C  385 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7663 (m-80)
REVERT: C  440 LYS cc_start: 0.7418 (ttmm) cc_final: 0.6667 (mptt)
REVERT: C  655 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6949 (mp)
REVERT: D   35 GLN cc_start: 0.7674 (tt0) cc_final: 0.7362 (tm-30)
REVERT: D  318 ASN cc_start: 0.7457 (t0) cc_final: 0.6931 (t0)
REVERT: D  322 ASN cc_start: 0.7807 (m110) cc_final: 0.7466 (m110)
REVERT: D  385 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7514 (m-80)
REVERT: D  440 LYS cc_start: 0.7250 (ttmm) cc_final: 0.6506 (mptt)
  outliers start: 25
  outliers final: 15
  residues processed: 134
  average time/residue: 1.0422
  time to fit residues: 154.9698
Evaluate side-chains
  137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain C residue  385 PHE
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  556 TYR
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  556 TYR
Chi-restraints excluded: chain D residue  721 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0070
   chunk 108 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0870
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
D 241 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.177273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143484 restraints weight = 7350.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.43
r_work: 0.3599 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10606  Z= 0.173
  Angle     :  0.572  11.124  14382  Z= 0.289
  Chirality :  0.044   0.204   1758
  Planarity :  0.005   0.079   1638
  Dihedral  : 12.773 137.093   2714
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.15 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.34 (0.24), residues: 1210
  helix:  1.80 (0.18), residues: 814
  sheet:  1.26 (0.70), residues: 34
  loop : -1.30 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 482 
 HIS   0.002   0.001   HIS D 728 
 PHE   0.016   0.001   PHE D 141 
 TYR   0.015   0.001   TYR C 105 
 ARG   0.002   0.000   ARG C 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 1.135 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7594 (tt0) cc_final: 0.7222 (tm-30)
REVERT: C   79 ARG cc_start: 0.6896 (mmm160) cc_final: 0.6030 (mtp180)
REVERT: C  307 THR cc_start: 0.8090 (m) cc_final: 0.7834 (p)
REVERT: C  318 ASN cc_start: 0.7411 (t0) cc_final: 0.6923 (t0)
REVERT: C  322 ASN cc_start: 0.7880 (m-40) cc_final: 0.7657 (m-40)
REVERT: C  385 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7471 (m-80)
REVERT: C  440 LYS cc_start: 0.7358 (ttmm) cc_final: 0.6587 (mptt)
REVERT: C  503 MET cc_start: 0.7421 (mmt) cc_final: 0.7159 (mmm)
REVERT: C  655 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6867 (mp)
REVERT: D   35 GLN cc_start: 0.7591 (tt0) cc_final: 0.7287 (tm-30)
REVERT: D  318 ASN cc_start: 0.7400 (t0) cc_final: 0.6863 (t0)
REVERT: D  322 ASN cc_start: 0.7776 (m110) cc_final: 0.7442 (m110)
REVERT: D  385 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7271 (m-80)
REVERT: D  440 LYS cc_start: 0.7174 (ttmm) cc_final: 0.6417 (mptt)
  outliers start: 18
  outliers final: 11
  residues processed: 134
  average time/residue: 0.9626
  time to fit residues: 142.2422
Evaluate side-chains
  130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  385 PHE
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  438 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 114 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0870
   chunk 58 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
D 241 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.175868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141950 restraints weight = 7322.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.43
r_work: 0.3574 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10606  Z= 0.190
  Angle     :  0.583  10.703  14382  Z= 0.297
  Chirality :  0.044   0.197   1758
  Planarity :  0.005   0.080   1638
  Dihedral  : 12.481 135.090   2714
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.04 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.24 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.22 (0.24), residues: 1210
  helix:  1.71 (0.18), residues: 826
  sheet:  1.25 (0.69), residues: 34
  loop : -1.46 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  74 
 HIS   0.002   0.001   HIS D 728 
 PHE   0.016   0.001   PHE C 141 
 TYR   0.016   0.001   TYR D 105 
 ARG   0.002   0.000   ARG C 185 

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.051 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.7671 (tt0) cc_final: 0.7302 (tm-30)
REVERT: C   79 ARG cc_start: 0.6923 (mmm160) cc_final: 0.6030 (mtp180)
REVERT: C  307 THR cc_start: 0.8191 (m) cc_final: 0.7917 (p)
REVERT: C  318 ASN cc_start: 0.7526 (t0) cc_final: 0.7075 (t0)
REVERT: C  320 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7064 (tt0)
REVERT: C  385 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7553 (m-80)
REVERT: C  440 LYS cc_start: 0.7430 (ttmm) cc_final: 0.6674 (mptt)
REVERT: C  503 MET cc_start: 0.7608 (mmt) cc_final: 0.7343 (mmm)
REVERT: C  655 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7009 (mp)
REVERT: D   35 GLN cc_start: 0.7605 (tt0) cc_final: 0.7327 (tm-30)
REVERT: D  318 ASN cc_start: 0.7472 (t0) cc_final: 0.6951 (t0)
REVERT: D  322 ASN cc_start: 0.7819 (m110) cc_final: 0.7495 (m110)
REVERT: D  385 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7470 (m-80)
REVERT: D  440 LYS cc_start: 0.7319 (ttmm) cc_final: 0.6589 (mptt)
  outliers start: 23
  outliers final: 17
  residues processed: 131
  average time/residue: 0.9954
  time to fit residues: 143.4300
Evaluate side-chains
  138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  320 GLU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain C residue  385 PHE
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  545 VAL
Chi-restraints excluded: chain C residue  556 TYR
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain C residue  721 THR
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  556 TYR
Chi-restraints excluded: chain D residue  721 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
D 241 ASN
D 689 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.170382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.136356 restraints weight = 7186.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.39
r_work: 0.3515 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  10606  Z= 0.299
  Angle     :  0.664  10.996  14382  Z= 0.337
  Chirality :  0.048   0.269   1758
  Planarity :  0.005   0.081   1638
  Dihedral  : 12.886 134.845   2714
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.04 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.15 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.85 (0.24), residues: 1210
  helix:  1.43 (0.18), residues: 824
  sheet:  1.06 (0.69), residues: 34
  loop : -1.60 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  74 
 HIS   0.003   0.001   HIS C 698 
 PHE   0.017   0.002   PHE D 401 
 TYR   0.019   0.002   TYR D 371 
 ARG   0.004   0.000   ARG C 185 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6685.93 seconds
wall clock time: 119 minutes 14.03 seconds (7154.03 seconds total)