Starting phenix.real_space_refine
on Wed Mar  4 00:21:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsv_30847/03_2026/7dsv_30847_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsv_30847/03_2026/7dsv_30847.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2026/7dsv_30847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2026/7dsv_30847.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2026/7dsv_30847_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2026/7dsv_30847_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    6194      2.51       5
     N    1522      2.21       5
     O    1596      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9340
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3672
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 15, 'TRANS': 447}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3672
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 15, 'TRANS': 447}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 915
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 167}
          Link IDs: {'PTRANS': 6, 'TRANS': 178}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 612
          Unresolved non-hydrogen angles: 771
          Unresolved non-hydrogen dihedrals: 499
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 20, 'PHE:plan': 13, 'HIS:plan': 4, 'GLN:plan1': 8, 'ARG:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 9}
          Unresolved non-hydrogen planarities: 372
    Chain: "A"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 83
          Unusual residues: {'LBN': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 333
          Unresolved non-hydrogen angles: 405
          Unresolved non-hydrogen dihedrals: 309
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'LBN:plan-1': 8, 'LBN:plan-2': 8, 'LBN:plan-3': 5}
          Unresolved non-hydrogen planarities: 76
    Chain: "B"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 83
          Unusual residues: {'LBN': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 333
          Unresolved non-hydrogen angles: 405
          Unresolved non-hydrogen dihedrals: 309
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'LBN:plan-1': 8, 'LBN:plan-2': 8, 'LBN:plan-3': 5}
          Unresolved non-hydrogen planarities: 76
  Restraints were copied for chains:
    D
  Residues with excluded nonbonded symmetry interactions: 16
    residue:
      pdb=" C10 LBN A 601 " occ=0.00
      ... (8 atoms not shown)
      pdb=" C7  LBN A 601 " occ=0.00
    residue:
      pdb=" C11 LBN A 602 " occ=0.00
      ... (13 atoms not shown)
      pdb=" C8  LBN A 602 " occ=0.00
    residue:
      pdb=" C11 LBN A 603 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C8  LBN A 603 " occ=0.00
    residue:
      pdb=" C11 LBN A 604 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C8  LBN A 604 " occ=0.00
    residue:
      pdb=" C11 LBN A 605 " occ=0.00
      ... (6 atoms not shown)
      pdb=" C8  LBN A 605 " occ=0.00
    residue:
      pdb=" C11 LBN A 606 " occ=0.00
      ... (6 atoms not shown)
      pdb=" C8  LBN A 606 " occ=0.00
    residue:
      pdb=" C11 LBN A 607 " occ=0.00
      ... (6 atoms not shown)
      pdb=" C8  LBN A 607 " occ=0.00
    residue:
      pdb=" C34 LBN A 608 " occ=0.00
      ... (8 atoms not shown)
      pdb=" C5  LBN A 608 " occ=0.00
    residue:
      pdb=" C34 LBN B 801 " occ=0.00
      ... (8 atoms not shown)
      pdb=" C5  LBN B 801 " occ=0.00
    residue:
      pdb=" C10 LBN B 802 " occ=0.00
      ... (8 atoms not shown)
      pdb=" C7  LBN B 802 " occ=0.00
    residue:
      pdb=" C11 LBN B 803 " occ=0.00
      ... (13 atoms not shown)
      pdb=" C8  LBN B 803 " occ=0.00
    residue:
      pdb=" C11 LBN B 804 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C8  LBN B 804 " occ=0.00
    ... (remaining 4 not shown)
  Time building chain proxies: 2.23, per 1000 atoms: 0.24
  Number of scatterers: 9340
  At special positions: 0
  Unit cell: (143, 73, 101, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1596      8.00
     N    1522      7.00
     C    6194      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: 0.79
  Conformation dependent library (CDL) restraints added in 260.3 milliseconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 0 sheets defined
      74.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 117
    Processing helix  chain 'A' and resid 130 through 150
      removed outlier: 3.678A  pdb=" N   LEU A 134 " --> pdb=" O   PRO A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 165 through 176
      removed outlier: 4.064A  pdb=" N   ILE A 169 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE A 176 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 185
      removed outlier: 3.504A  pdb=" N   ASN A 185 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 214
      removed outlier: 3.547A  pdb=" N   ILE A 189 " --> pdb=" O   ASN A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 235
      removed outlier: 3.549A  pdb=" N   PHE A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 245
    Processing helix  chain 'A' and resid 252 through 281
      removed outlier: 3.644A  pdb=" N   ILE A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 320
      removed outlier: 3.745A  pdb=" N   PHE A 299 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 348
      removed outlier: 3.586A  pdb=" N   VAL A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 367
      Proline residue:  A 365  - end of helix
    Processing helix  chain 'A' and resid 372 through 404
    Processing helix  chain 'A' and resid 410 through 438
      removed outlier: 3.997A  pdb=" N   LYS A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 454
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 476 through 494
    Processing helix  chain 'A' and resid 499 through 504
      removed outlier: 3.592A  pdb=" N   ASP A 504 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 539
    Processing helix  chain 'A' and resid 543 through 558
    Processing helix  chain 'B' and resid 100 through 117
    Processing helix  chain 'B' and resid 130 through 150
      removed outlier: 3.679A  pdb=" N   LEU B 134 " --> pdb=" O   PRO B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 165
    Processing helix  chain 'B' and resid 165 through 176
      removed outlier: 4.064A  pdb=" N   ILE B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   PHE B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 185
      removed outlier: 3.504A  pdb=" N   ASN B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 214
      removed outlier: 3.546A  pdb=" N   ILE B 189 " --> pdb=" O   ASN B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 235
      removed outlier: 3.549A  pdb=" N   PHE B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 245
    Processing helix  chain 'B' and resid 252 through 281
      removed outlier: 3.644A  pdb=" N   ILE B 257 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 271 " --> pdb=" O   ASP B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 320
      removed outlier: 3.745A  pdb=" N   PHE B 299 " --> pdb=" O   PHE B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 3.587A  pdb=" N   VAL B 334 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE B 348 " --> pdb=" O   SER B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 367
      Proline residue:  B 365  - end of helix
    Processing helix  chain 'B' and resid 372 through 404
    Processing helix  chain 'B' and resid 410 through 438
      removed outlier: 3.997A  pdb=" N   LYS B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 454
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 476 through 494
    Processing helix  chain 'B' and resid 499 through 504
      removed outlier: 3.592A  pdb=" N   ASP B 504 " --> pdb=" O   ARG B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 539
    Processing helix  chain 'B' and resid 543 through 558
    Processing helix  chain 'D' and resid 16 through 21
    Processing helix  chain 'D' and resid 24 through 40
      removed outlier: 4.114A  pdb=" N   LYS D  40 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 53
    Processing helix  chain 'D' and resid 62 through 71
      removed outlier: 4.307A  pdb=" N   PHE D  71 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 89
      removed outlier: 4.196A  pdb=" N   HIS D  89 " --> pdb=" O   ARG D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 100
    Processing helix  chain 'D' and resid 110 through 123
      removed outlier: 3.743A  pdb=" N   LEU D 115 " --> pdb=" O   ARG D 111 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA D 118 " --> pdb=" O   LYS D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 143
    Processing helix  chain 'D' and resid 148 through 164
    Processing helix  chain 'D' and resid 172 through 182
      removed outlier: 3.645A  pdb=" N   LYS D 178 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LYS D 182 " --> pdb=" O   LYS D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 189
      removed outlier: 3.592A  pdb=" N   LYS D 188 " --> pdb=" O   ASP D 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 24 through 40
      removed outlier: 4.114A  pdb=" N   LYS C  40 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 53
    Processing helix  chain 'C' and resid 62 through 71
      removed outlier: 4.307A  pdb=" N   PHE C  71 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 4.195A  pdb=" N   HIS C  89 " --> pdb=" O   ARG C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 100
    Processing helix  chain 'C' and resid 110 through 123
      removed outlier: 3.743A  pdb=" N   LEU C 115 " --> pdb=" O   ARG C 111 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA C 118 " --> pdb=" O   LYS C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 143
    Processing helix  chain 'C' and resid 148 through 164
    Processing helix  chain 'C' and resid 172 through 182
      removed outlier: 3.644A  pdb=" N   LYS C 178 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LYS C 182 " --> pdb=" O   LYS C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 189
      removed outlier: 3.591A  pdb=" N   LYS C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)

    666 hydrogen bonds defined for protein.
    1968 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: 1.39

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1470
        1.31 -     1.44: 2546
        1.44 -     1.56: 5446
        1.56 -     1.69: 22
        1.69 -     1.81: 44
  Bond restraints: 9528
  Sorted by residual:
  bond pdb=" C   GLU D  16 "
       pdb=" O   GLU D  16 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.050 1.19e-02 7.06e+03 1.79e+01
  bond pdb=" C   GLU C  16 "
       pdb=" O   GLU C  16 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.19e-02 7.06e+03 1.77e+01
  bond pdb=" N   ASP C  95 "
       pdb=" CA  ASP C  95 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.046 1.29e-02 6.01e+03 1.29e+01
  bond pdb=" N   ASP D  95 "
       pdb=" CA  ASP D  95 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.046 1.29e-02 6.01e+03 1.28e+01
  bond pdb=" C5  LBN B 805 "
       pdb=" C8  LBN B 805 "
    ideal  model  delta    sigma   weight residual
    1.497  1.567 -0.070 2.00e-02 2.50e+03 1.23e+01
  ... (remaining 9523 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 12197
        2.15 -     4.31: 642
        4.31 -     6.46: 92
        6.46 -     8.62: 25
        8.62 -    10.77: 4
  Bond angle restraints: 12960
  Sorted by residual:
  angle pdb=" CA  LYS C  98 "
        pdb=" C   LYS C  98 "
        pdb=" N   SER C  99 "
      ideal   model   delta    sigma   weight residual
     118.38  108.99    9.39 1.30e+00 5.92e-01 5.22e+01
  angle pdb=" CA  LYS D  98 "
        pdb=" C   LYS D  98 "
        pdb=" N   SER D  99 "
      ideal   model   delta    sigma   weight residual
     118.38  109.05    9.33 1.30e+00 5.92e-01 5.15e+01
  angle pdb=" C   LYS D  98 "
        pdb=" N   SER D  99 "
        pdb=" CA  SER D  99 "
      ideal   model   delta    sigma   weight residual
     122.09  132.86  -10.77 1.79e+00 3.12e-01 3.62e+01
  angle pdb=" C   LYS C  98 "
        pdb=" N   SER C  99 "
        pdb=" CA  SER C  99 "
      ideal   model   delta    sigma   weight residual
     122.09  132.82  -10.73 1.79e+00 3.12e-01 3.59e+01
  angle pdb=" O   LYS C  98 "
        pdb=" C   LYS C  98 "
        pdb=" N   SER C  99 "
      ideal   model   delta    sigma   weight residual
     122.42  130.08   -7.66 1.31e+00 5.83e-01 3.42e+01
  ... (remaining 12955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.30: 4795
       14.30 -    28.61: 464
       28.61 -    42.91: 155
       42.91 -    57.21: 32
       57.21 -    71.52: 12
  Dihedral angle restraints: 5458
    sinusoidal: 1734
      harmonic: 3724
  Sorted by residual:
  dihedral pdb=" CA  ALA D 171 "
           pdb=" C   ALA D 171 "
           pdb=" N   SER D 172 "
           pdb=" CA  SER D 172 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.32  -27.68     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  ALA C 171 "
           pdb=" C   ALA C 171 "
           pdb=" N   SER C 172 "
           pdb=" CA  SER C 172 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.34  -27.66     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  LYS D 129 "
           pdb=" C   LYS D 129 "
           pdb=" N   ILE D 130 "
           pdb=" CA  ILE D 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.02   24.98     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 5455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1216
       0.064 -    0.127: 292
       0.127 -    0.191: 45
       0.191 -    0.254: 11
       0.254 -    0.318: 8
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CA  GLU C  20 "
            pdb=" N   GLU C  20 "
            pdb=" C   GLU C  20 "
            pdb=" CB  GLU C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  GLU D  20 "
            pdb=" N   GLU D  20 "
            pdb=" C   GLU D  20 "
            pdb=" CB  GLU D  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  ASN C 109 "
            pdb=" N   ASN C 109 "
            pdb=" C   ASN C 109 "
            pdb=" CB  ASN C 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.41e+00
  ... (remaining 1569 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D  99 "    0.037 2.00e-02 2.50e+03   7.16e-02 5.13e+01
        pdb=" C   SER D  99 "   -0.124 2.00e-02 2.50e+03
        pdb=" O   SER D  99 "    0.044 2.00e-02 2.50e+03
        pdb=" N   LYS D 100 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C  99 "    0.037 2.00e-02 2.50e+03   7.16e-02 5.12e+01
        pdb=" C   SER C  99 "   -0.124 2.00e-02 2.50e+03
        pdb=" O   SER C  99 "    0.044 2.00e-02 2.50e+03
        pdb=" N   LYS C 100 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D  96 "    0.017 2.00e-02 2.50e+03   3.61e-02 1.30e+01
        pdb=" C   ASN D  96 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   ASN D  96 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU D  97 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 604
        2.72 -     3.27: 10053
        3.27 -     3.81: 15305
        3.81 -     4.36: 18162
        4.36 -     4.90: 31162
  Nonbonded interactions: 75286
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 367 "
            pdb=" CG  GLU B 368 "
     model   vdw
     2.180 3.440
  nonbonded pdb=" O   VAL A 367 "
            pdb=" CG  GLU A 368 "
     model   vdw
     2.181 3.440
  nonbonded pdb=" O   SER A 375 "
            pdb=" OG1 THR A 378 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   SER B 375 "
            pdb=" OG1 THR B 378 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   PHE B 162 "
            pdb=" OH  TYR B 342 "
     model   vdw
     2.305 3.040
  ... (remaining 75281 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 87 through 601 or resid 603 through 607))
  selection = (chain 'B' and (resid 87 through 801 or (resid 803 through 804 and (name C11 or  \ 
name C14 or name C17 or name C20 or name C22 or name C23 or name C24 or name C40 \ 
 or name C41 or name C42 or name C5 or name C8 )) or (resid 805 through 807 and  \ 
(name C11 or name C14 or name C17 or name C20 or name C22 or name C23 or name C2 \ 
4 or name C8 ))))
}
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=0.00 max=1.00 mean=0.98
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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.570
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
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      :  0.008   0.070   9528  Z= 0.467
  Angle     :  1.061  10.769  12960  Z= 0.658
  Chirality :  0.061   0.318   1572
  Planarity :  0.006   0.072   1620
  Dihedral  : 13.922  71.516   3054
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  1.37 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.22), residues: 1284
  helix: -0.25 (0.16), residues: 920
  sheet:  None (None), residues: 0
  loop : -2.20 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 364 
 TYR   0.012   0.001   TYR A 283 
 PHE   0.018   0.002   PHE A 119 
 TRP   0.005   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00833 ( 9528)
  covalent geometry    : angle       1.06103 (12960)
  hydrogen bonds       : bond        0.11436 (  666)
  hydrogen bonds       : angle       6.39899 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 ILE cc_start: 0.8509 (tt) cc_final: 0.8269 (tt)
REVERT: A  419 LEU cc_start: 0.8808 (tt) cc_final: 0.8520 (tt)
REVERT: A  546 TRP cc_start: 0.3155 (OUTLIER) cc_final: 0.2616 (m100)
REVERT: B  125 ILE cc_start: 0.8493 (tt) cc_final: 0.8228 (tt)
REVERT: B  546 TRP cc_start: 0.2826 (OUTLIER) cc_final: 0.2393 (m100)
  outliers start: 14
  outliers final: 7
  residues processed: 118
  average time/residue: 0.0790
  time to fit residues: 13.9363
Evaluate side-chains
  97 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  549 LYS
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  538 CYS
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  546 TRP
Chi-restraints excluded: chain B residue  549 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
A 544 HIS
A 545 HIS
B 227 ASN
B 250 HIS
B 519 ASN
B 544 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.195546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.180265 restraints weight = 8837.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 0.58
r_work: 0.3594 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9528  Z= 0.142
  Angle     :  0.546   6.576  12960  Z= 0.293
  Chirality :  0.043   0.200   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  7.674  62.918   1474
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.98 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.24), residues: 1284
  helix:  1.07 (0.17), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.68 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 364 
 TYR   0.009   0.001   TYR A 274 
 PHE   0.015   0.001   PHE B 382 
 TRP   0.006   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9528)
  covalent geometry    : angle       0.54626 (12960)
  hydrogen bonds       : bond        0.03986 (  666)
  hydrogen bonds       : angle       4.82374 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  364 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7998 (ttt180)
REVERT: A  419 LEU cc_start: 0.8863 (tt) cc_final: 0.8640 (tt)
REVERT: B  125 ILE cc_start: 0.8498 (tt) cc_final: 0.8294 (tt)
  outliers start: 6
  outliers final: 2
  residues processed: 102
  average time/residue: 0.0712
  time to fit residues: 11.2898
Evaluate side-chains
  96 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain B residue  128 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 90 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0050
   chunk 95 optimal weight:   40.0000
   chunk 61 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 105 optimal weight:   50.0000
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS

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 = 0.194437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.180711 restraints weight = 8833.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 0.58
r_work: 0.3615 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9528  Z= 0.142
  Angle     :  0.529   6.859  12960  Z= 0.279
  Chirality :  0.042   0.213   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  7.012  63.623   1454
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.10 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.24), residues: 1284
  helix:  1.50 (0.18), residues: 894
  sheet:  None (None), residues: 0
  loop : -1.59 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 180 
 TYR   0.009   0.001   TYR A 274 
 PHE   0.014   0.001   PHE B 382 
 TRP   0.006   0.001   TRP A 386 
 HIS   0.003   0.001   HIS B 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9528)
  covalent geometry    : angle       0.52891 (12960)
  hydrogen bonds       : bond        0.03720 (  666)
  hydrogen bonds       : angle       4.56434 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   87 LYS cc_start: 0.6655 (tttt) cc_final: 0.6205 (tttp)
REVERT: A  364 ARG cc_start: 0.8293 (ttt90) cc_final: 0.8058 (ttt180)
REVERT: A  457 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8149 (pt)
REVERT: B  125 ILE cc_start: 0.8619 (tt) cc_final: 0.8392 (tt)
REVERT: B  346 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7301 (mm-30)
REVERT: B  364 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7952 (ttt180)
  outliers start: 17
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0750
  time to fit residues: 12.3441
Evaluate side-chains
  110 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  457 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 125 optimal weight:   40.0000
   chunk 86 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.191683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.176365 restraints weight = 8868.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 0.62
r_work: 0.3551 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9528  Z= 0.191
  Angle     :  0.564   7.098  12960  Z= 0.297
  Chirality :  0.044   0.203   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  7.560  66.452   1454
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 11.97 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.24), residues: 1284
  helix:  1.38 (0.17), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.56 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 364 
 TYR   0.010   0.001   TYR A 274 
 PHE   0.016   0.001   PHE B 382 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.004   0.001   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9528)
  covalent geometry    : angle       0.56450 (12960)
  hydrogen bonds       : bond        0.03922 (  666)
  hydrogen bonds       : angle       4.69761 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B  125 ILE cc_start: 0.8667 (tt) cc_final: 0.8423 (tt)
REVERT: B  346 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7361 (mm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 109
  average time/residue: 0.0771
  time to fit residues: 12.6903
Evaluate side-chains
  111 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 98 optimal weight:   40.0000
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 126 optimal weight:   10.0000
   chunk 84 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 118 optimal weight:   40.0000
   chunk 36 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.193217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.172017 restraints weight = 8885.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 0.49
r_work: 0.3458 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9528  Z= 0.145
  Angle     :  0.514   6.759  12960  Z= 0.271
  Chirality :  0.042   0.193   1572
  Planarity :  0.004   0.054   1620
  Dihedral  :  7.054  67.593   1454
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.09 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.24), residues: 1284
  helix:  1.60 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.49 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 440 
 TYR   0.009   0.001   TYR B 274 
 PHE   0.013   0.001   PHE B 382 
 TRP   0.006   0.001   TRP A 386 
 HIS   0.002   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9528)
  covalent geometry    : angle       0.51414 (12960)
  hydrogen bonds       : bond        0.03553 (  666)
  hydrogen bonds       : angle       4.47354 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.361 
Fit side-chains
REVERT: B  122 ILE cc_start: 0.8107 (mt) cc_final: 0.7856 (mp)
REVERT: B  125 ILE cc_start: 0.8628 (tt) cc_final: 0.8367 (tt)
REVERT: B  346 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7262 (mm-30)
REVERT: B  432 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8356 (mt)
  outliers start: 21
  outliers final: 12
  residues processed: 113
  average time/residue: 0.0751
  time to fit residues: 13.1263
Evaluate side-chains
  113 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  457 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 105 optimal weight:   50.0000
   chunk 30 optimal weight:    1.9990
   chunk 107 optimal weight:   50.0000
   chunk 54 optimal weight:    0.6980
   chunk 92 optimal weight:   20.0000
   chunk 48 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
A 325 HIS
B 250 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.189616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.167268 restraints weight = 8901.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 0.49
r_work: 0.3422 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9528  Z= 0.215
  Angle     :  0.583   7.454  12960  Z= 0.304
  Chirality :  0.044   0.182   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  7.620  68.957   1454
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.09 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.24), residues: 1284
  helix:  1.36 (0.17), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.41 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.010   0.001   TYR B 274 
 PHE   0.015   0.002   PHE A 463 
 TRP   0.007   0.001   TRP A 386 
 HIS   0.004   0.001   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 9528)
  covalent geometry    : angle       0.58300 (12960)
  hydrogen bonds       : bond        0.03942 (  666)
  hydrogen bonds       : angle       4.71349 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.309 
Fit side-chains
  outliers start: 24
  outliers final: 17
  residues processed: 107
  average time/residue: 0.0686
  time to fit residues: 11.4972
Evaluate side-chains
  110 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  473 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 97 optimal weight:   40.0000
   chunk 100 optimal weight:   10.0000
   chunk 102 optimal weight:   40.0000
   chunk 112 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS
B 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.189472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.172968 restraints weight = 9010.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 0.59
r_work: 0.3517 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   9528  Z= 0.223
  Angle     :  0.586   8.205  12960  Z= 0.305
  Chirality :  0.044   0.170   1572
  Planarity :  0.005   0.056   1620
  Dihedral  :  7.638  66.957   1454
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.59 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.24), residues: 1284
  helix:  1.34 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.46 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 425 
 TYR   0.011   0.001   TYR B 274 
 PHE   0.015   0.002   PHE B 119 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.004   0.001   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 9528)
  covalent geometry    : angle       0.58648 (12960)
  hydrogen bonds       : bond        0.03893 (  666)
  hydrogen bonds       : angle       4.71167 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.253 
Fit side-chains
  outliers start: 23
  outliers final: 17
  residues processed: 109
  average time/residue: 0.0616
  time to fit residues: 11.0146
Evaluate side-chains
  110 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  473 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 63 optimal weight:    0.5980
   chunk 101 optimal weight:   50.0000
   chunk 94 optimal weight:    9.9990
   chunk 36 optimal weight:    0.6980
   chunk 120 optimal weight:   30.0000
   chunk 124 optimal weight:   20.0000
   chunk 99 optimal weight:   30.0000
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.193215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.174522 restraints weight = 8871.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 0.64
r_work: 0.3514 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9528  Z= 0.135
  Angle     :  0.522   7.963  12960  Z= 0.274
  Chirality :  0.041   0.169   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  6.908  67.260   1454
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.84 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.24), residues: 1284
  helix:  1.65 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.39 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 440 
 TYR   0.009   0.001   TYR B 274 
 PHE   0.014   0.001   PHE B 119 
 TRP   0.004   0.001   TRP A 386 
 HIS   0.002   0.001   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9528)
  covalent geometry    : angle       0.52219 (12960)
  hydrogen bonds       : bond        0.03479 (  666)
  hydrogen bonds       : angle       4.46440 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.305 
Fit side-chains
REVERT: B  213 LEU cc_start: 0.8505 (mt) cc_final: 0.8269 (mt)
REVERT: B  346 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7572 (mm-30)
REVERT: B  432 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8366 (mt)
  outliers start: 16
  outliers final: 14
  residues processed: 105
  average time/residue: 0.0631
  time to fit residues: 10.6407
Evaluate side-chains
  109 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  473 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 95 optimal weight:   30.0000
   chunk 23 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 119 optimal weight:    0.0040
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A 495 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.193811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.178725 restraints weight = 8869.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 0.60
r_work: 0.3569 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9528  Z= 0.134
  Angle     :  0.518   8.548  12960  Z= 0.270
  Chirality :  0.041   0.170   1572
  Planarity :  0.004   0.056   1620
  Dihedral  :  6.687  66.178   1454
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.08 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.24), residues: 1284
  helix:  1.79 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 440 
 TYR   0.010   0.001   TYR B 274 
 PHE   0.013   0.001   PHE B 119 
 TRP   0.004   0.001   TRP A 386 
 HIS   0.002   0.001   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9528)
  covalent geometry    : angle       0.51752 (12960)
  hydrogen bonds       : bond        0.03419 (  666)
  hydrogen bonds       : angle       4.34143 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7193 (mm-30)
REVERT: B  213 LEU cc_start: 0.8447 (mt) cc_final: 0.8225 (mt)
REVERT: B  346 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7250 (mm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0623
  time to fit residues: 11.3363
Evaluate side-chains
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  473 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 123 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 1 optimal weight:    0.2980
   chunk 108 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 111 optimal weight:   40.0000
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
A 495 GLN
B 250 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.189429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.169680 restraints weight = 8887.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 0.60
r_work: 0.3436 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9528  Z= 0.207
  Angle     :  0.581   8.930  12960  Z= 0.302
  Chirality :  0.044   0.157   1572
  Planarity :  0.004   0.057   1620
  Dihedral  :  7.238  64.211   1454
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.58 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.24), residues: 1284
  helix:  1.53 (0.17), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.32 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 440 
 TYR   0.011   0.001   TYR B 274 
 PHE   0.015   0.002   PHE B 382 
 TRP   0.003   0.001   TRP B 411 
 HIS   0.004   0.001   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 9528)
  covalent geometry    : angle       0.58134 (12960)
  hydrogen bonds       : bond        0.03833 (  666)
  hydrogen bonds       : angle       4.63430 ( 1968)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.326 
Fit side-chains
  outliers start: 17
  outliers final: 14
  residues processed: 105
  average time/residue: 0.0663
  time to fit residues: 11.1722
Evaluate side-chains
  111 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  473 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 107 optimal weight:   50.0000
   chunk 112 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 89 optimal weight:   20.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 495 GLN
B 495 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.193245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.177993 restraints weight = 8797.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 0.60
r_work: 0.3569 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9528  Z= 0.129
  Angle     :  0.523   8.744  12960  Z= 0.272
  Chirality :  0.041   0.164   1572
  Planarity :  0.004   0.056   1620
  Dihedral  :  6.699  64.753   1454
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.96 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.25), residues: 1284
  helix:  1.81 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.29 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 440 
 TYR   0.009   0.001   TYR A 274 
 PHE   0.013   0.001   PHE B 382 
 TRP   0.003   0.001   TRP A 386 
 HIS   0.002   0.000   HIS B 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9528)
  covalent geometry    : angle       0.52271 (12960)
  hydrogen bonds       : bond        0.03419 (  666)
  hydrogen bonds       : angle       4.35911 ( 1968)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.38 seconds
wall clock time: 28 minutes 7.41 seconds (1687.41 seconds total)