Starting phenix.real_space_refine
on Fri Mar 14 02:58:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsv_30847/03_2025/7dsv_30847_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsv_30847/03_2025/7dsv_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_2025/7dsv_30847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2025/7dsv_30847.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2025/7dsv_30847_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsv_30847/03_2025/7dsv_30847_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 14}
          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-2': 8, 'LBN:plan-3': 5, 'LBN:plan-1': 8}
          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-2': 8, 'LBN:plan-3': 5, 'LBN:plan-1': 8}
          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: 6.44, per 1000 atoms: 0.69
  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.01
  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: 2.75

  Time building geometry restraints manager: 3.05 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 87 through 558 or resid 601 or resid 603 through 607))
  selection = (chain 'B' and (resid 87 through 558 or resid 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 C2 \ 
4 or name C40 or name C41 or name C42 or name C5 or name C8 )) or (resid 805 thr \ 
ough 807 and (name C11 or name C14 or name C17 or name C20 or name C22 or name C \ 
23 or name C24 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:             1.080
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.070
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.030
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.050
-------------------------------------------------------------------------------
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= 0.564
  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 (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: -1.28 (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
 TRP   0.005   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 545 
 PHE   0.018   0.002   PHE A 119 
 TYR   0.012   0.001   TYR A 283 
 ARG   0.012   0.001   ARG B 364 

*********************** 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  : 1.005 
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: 0.8807 (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: 0.2083
  time to fit residues: 36.4121
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  : 0.909 
-------------------------------------------------------------------------------
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 108 optimal weight:   30.0000
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 116 optimal weight:    7.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 250 HIS
B 519 ASN
B 544 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.194499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.177577 restraints weight = 8832.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 0.59
r_work: 0.3541 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9528  Z= 0.231
  Angle     :  0.557   6.554  12960  Z= 0.298
  Chirality :  0.043   0.205   1572
  Planarity :  0.004   0.056   1620
  Dihedral  :  7.796  63.660   1474
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.73 %
    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 (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:  0.34 (0.24), residues: 1284
  helix:  1.03 (0.17), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.69 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 545 
 PHE   0.015   0.001   PHE B 382 
 TYR   0.010   0.001   TYR A 274 
 ARG   0.006   0.001   ARG A 364 

*********************** 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
  107 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A  125 ILE cc_start: 0.8551 (tt) cc_final: 0.8345 (tt)
REVERT: A  364 ARG cc_start: 0.8288 (ttt90) cc_final: 0.8054 (ttt180)
REVERT: A  419 LEU cc_start: 0.8884 (tt) cc_final: 0.8674 (tt)
REVERT: B  125 ILE cc_start: 0.8521 (tt) cc_final: 0.8309 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1624
  time to fit residues: 25.5494
Evaluate side-chains
  96 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  152 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 96 optimal weight:   50.0000
   chunk 90 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 124 optimal weight:    5.9990
   chunk 111 optimal weight:   50.0000
   chunk 103 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.189365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.175075 restraints weight = 8970.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 0.60
r_work: 0.3508 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   9528  Z= 0.385
  Angle     :  0.624   7.447  12960  Z= 0.324
  Chirality :  0.046   0.216   1572
  Planarity :  0.005   0.058   1620
  Dihedral  :  8.189  66.588   1454
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.60 %
    Favored  : 86.66 %
  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:  0.33 (0.24), residues: 1284
  helix:  0.97 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop : -1.64 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 386 
 HIS   0.005   0.001   HIS B 545 
 PHE   0.015   0.002   PHE A 119 
 TYR   0.010   0.001   TYR A 274 
 ARG   0.004   0.001   ARG A 180 

*********************** 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
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   87 LYS cc_start: 0.6899 (tttt) cc_final: 0.6416 (tttp)
REVERT: A  125 ILE cc_start: 0.8655 (tt) cc_final: 0.8431 (tt)
REVERT: A  346 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7062 (mm-30)
REVERT: B  125 ILE cc_start: 0.8665 (tt) cc_final: 0.8437 (tt)
REVERT: B  346 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7058 (mm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1729
  time to fit residues: 28.2253
Evaluate side-chains
  108 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 119 optimal weight:    0.7980
   chunk 112 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0030
   chunk 82 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.195100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.178133 restraints weight = 8803.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 0.64
r_work: 0.3541 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.2057

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= 0.185
  Angle     :  0.497   6.611  12960  Z= 0.264
  Chirality :  0.041   0.192   1572
  Planarity :  0.004   0.052   1620
  Dihedral  :  7.036  64.708   1454
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.22 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.97 (0.24), residues: 1284
  helix:  1.48 (0.18), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.48 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 386 
 HIS   0.002   0.000   HIS B 545 
 PHE   0.016   0.001   PHE B 382 
 TYR   0.009   0.001   TYR A 274 
 ARG   0.003   0.000   ARG A 364 

*********************** 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
  114 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  125 ILE cc_start: 0.8582 (tt) cc_final: 0.8326 (tt)
REVERT: A  346 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7302 (mm-30)
REVERT: B  122 ILE cc_start: 0.8120 (mt) cc_final: 0.7850 (mp)
REVERT: B  125 ILE cc_start: 0.8599 (tt) cc_final: 0.8363 (tt)
REVERT: B  346 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7347 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1722
  time to fit residues: 28.5557
Evaluate side-chains
  105 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  473 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 118 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 107 optimal weight:   50.0000
   chunk 98 optimal weight:   50.0000
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4018 r_free = 0.4018 target = 0.192579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.176934 restraints weight = 8835.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 0.60
r_work: 0.3549 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9528  Z= 0.241
  Angle     :  0.524   7.082  12960  Z= 0.276
  Chirality :  0.042   0.194   1572
  Planarity :  0.004   0.054   1620
  Dihedral  :  7.265  67.551   1454
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 12.97 %
    Favored  : 84.16 %
  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:  1.06 (0.24), residues: 1284
  helix:  1.57 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.49 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 545 
 PHE   0.013   0.001   PHE A 119 
 TYR   0.009   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 180 

*********************** 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
  128 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7799 (mm-30)
REVERT: B  346 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7862 (mm-30)
  outliers start: 23
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1893
  time to fit residues: 34.5267
Evaluate side-chains
  114 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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  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  457 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 114 optimal weight:   30.0000
   chunk 41 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 111 optimal weight:   40.0000
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 325 HIS
B 519 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.193828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.172558 restraints weight = 8818.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 0.53
r_work: 0.3475 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9528  Z= 0.214
  Angle     :  0.506   7.069  12960  Z= 0.268
  Chirality :  0.041   0.184   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  6.975  67.633   1454
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.84 %
    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 (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:  1.23 (0.24), residues: 1284
  helix:  1.70 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.43 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.002   0.001   HIS B 545 
 PHE   0.012   0.001   PHE B 119 
 TYR   0.009   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 180 

*********************** 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
  115 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7554 (mm-30)
REVERT: B  125 ILE cc_start: 0.8695 (tt) cc_final: 0.8434 (tt)
REVERT: B  346 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7513 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1578
  time to fit residues: 25.5433
Evaluate side-chains
  112 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:   50.0000
   chunk 60 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 127 optimal weight:   30.0000
   chunk 72 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0870
   chunk 56 optimal weight:    1.9990
   chunk 103 optimal weight:   40.0000
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.5760

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.194919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.176592 restraints weight = 8898.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 0.55
r_work: 0.3523 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2562

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= 0.187
  Angle     :  0.495   7.227  12960  Z= 0.262
  Chirality :  0.041   0.164   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  6.595  67.177   1454
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.84 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.25), residues: 1284
  helix:  1.84 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.37 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 386 
 HIS   0.002   0.000   HIS B 545 
 PHE   0.012   0.001   PHE B 119 
 TYR   0.008   0.001   TYR B 274 
 ARG   0.002   0.000   ARG A 180 

*********************** 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
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7535 (mm-30)
REVERT: B  346 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7502 (mm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1536
  time to fit residues: 26.0423
Evaluate side-chains
  109 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
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 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  457 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 122 optimal weight:   40.0000
   chunk 92 optimal weight:    7.9990
   chunk 124 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 90 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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
A 540 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.193173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.174947 restraints weight = 8988.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 0.53
r_work: 0.3509 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9528  Z= 0.226
  Angle     :  0.518   7.980  12960  Z= 0.273
  Chirality :  0.041   0.163   1572
  Planarity :  0.004   0.056   1620
  Dihedral  :  6.680  66.774   1454
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.21 %
    Favored  : 81.55 %
  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:  1.38 (0.24), residues: 1284
  helix:  1.80 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 386 
 HIS   0.002   0.001   HIS B 545 
 PHE   0.014   0.001   PHE A 119 
 TYR   0.009   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 180 

*********************** 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
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: B  346 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7356 (mm-30)
  outliers start: 18
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1548
  time to fit residues: 25.6871
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  : 0.988 
-------------------------------------------------------------------------------
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  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  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  457 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 105 optimal weight:   30.0000
   chunk 57 optimal weight:    2.9990
   chunk 122 optimal weight:   50.0000
   chunk 62 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 85 optimal weight:    0.5980
   chunk 112 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 84 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.193793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.179197 restraints weight = 8827.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 0.57
r_work: 0.3594 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9528  Z= 0.213
  Angle     :  0.511   8.490  12960  Z= 0.269
  Chirality :  0.041   0.163   1572
  Planarity :  0.004   0.056   1620
  Dihedral  :  6.509  66.256   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  : 16.58 %
    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 (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:  1.51 (0.25), residues: 1284
  helix:  1.89 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.29 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.013   0.001   PHE A 119 
 TYR   0.008   0.001   TYR B 274 
 ARG   0.002   0.000   ARG B 440 

*********************** 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
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7235 (mm-30)
REVERT: B  346 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7223 (mm-30)
  outliers start: 17
  outliers final: 17
  residues processed: 106
  average time/residue: 0.1521
  time to fit residues: 25.3648
Evaluate side-chains
  116 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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  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  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  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  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 94 optimal weight:    2.9990
   chunk 113 optimal weight:   20.0000
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0670
   chunk 120 optimal weight:   30.0000
   chunk 44 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 116 optimal weight:   40.0000
   chunk 90 optimal weight:    0.4980
   chunk 101 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.4518

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.195958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.179671 restraints weight = 8953.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 0.62
r_work: 0.3579 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9528  Z= 0.170
  Angle     :  0.492   8.355  12960  Z= 0.259
  Chirality :  0.040   0.168   1572
  Planarity :  0.004   0.055   1620
  Dihedral  :  6.186  66.731   1454
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.21 %
    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 (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:  1.71 (0.25), residues: 1284
  helix:  2.03 (0.18), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.18 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 386 
 HIS   0.002   0.000   HIS A 540 
 PHE   0.011   0.001   PHE A 119 
 TYR   0.008   0.001   TYR B 274 
 ARG   0.002   0.000   ARG A 180 

********************** 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
  118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A  346 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: B  346 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7466 (mm-30)
  outliers start: 15
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1827
  time to fit residues: 30.8909
Evaluate side-chains
  113 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
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  188 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 A residue  473 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  188 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  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 120 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 124 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 97 optimal weight:   30.0000
   chunk 16 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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
B 495 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.187631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.171697 restraints weight = 8960.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 0.59
r_work: 0.3509 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   9528  Z= 0.471
  Angle     :  0.643   8.981  12960  Z= 0.333
  Chirality :  0.047   0.192   1572
  Planarity :  0.005   0.056   1620
  Dihedral  :  7.525  64.603   1454
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.21 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 1284
  helix:  1.39 (0.17), residues: 916
  sheet:  None (None), residues: 0
  loop : -1.54 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 386 
 HIS   0.005   0.001   HIS B 545 
 PHE   0.017   0.002   PHE A 463 
 TYR   0.011   0.002   TYR B 454 
 ARG   0.005   0.001   ARG B 425 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3673.42 seconds
wall clock time: 65 minutes 46.60 seconds (3946.60 seconds total)