Starting phenix.real_space_refine
on Thu Jul  2 03:02:02 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl6_27497/07_2026/8dl6_27497.map"
  }
  resolution = 3.0
  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=   0.014 sd=   0.076
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      34      5.16       5
     C    3944      2.51       5
     N    1045      2.21       5
     O    1147      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6171
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3384
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 442, 3377
          Classifications: {'peptide': 442}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 431}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 442, 3377
          Classifications: {'peptide': 442}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 431}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 3439
    Chain: "C"
      Number of atoms: 1348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1348
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 411
          Unresolved non-hydrogen dihedrals: 270
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 8, 'TYR:plan': 4, 'ASP:plan': 6, 'TRP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 177
    Chain: "D"
      Number of atoms: 1437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1437
          Classifications: {'peptide': 219}
          Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81}
          Link IDs: {'PTRANS': 14, 'TRANS': 204}
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 252
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 91
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATHR A 334 " occ=0.71
      ... (12 atoms not shown)
      pdb=" CG2BTHR A 334 " occ=0.29
  Time building chain proxies: 2.24, per 1000 atoms: 0.36
  Number of scatterers: 6171
  At special positions: 0
  Unit cell: (75.9, 72.6, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      34     16.00
     O    1147      8.00
     N    1045      7.00
     C    3944      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 367 " - pdb=" SG  CYS A 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D 115 " distance=2.03

  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: 0.48
  Conformation dependent library (CDL) restraints added in 465.1 milliseconds
  

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 9 sheets defined
      49.9% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 23
    Processing helix  chain 'A' and resid 24 through 55
      removed outlier: 4.066A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 85
      removed outlier: 3.882A  pdb=" N   VAL A  74 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ASP A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
    Processing helix  chain 'A' and resid 116 through 124
      removed outlier: 4.664A  pdb=" N   TYR A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 163
      removed outlier: 4.387A  pdb=" N   THR A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 197
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 228
      removed outlier: 3.911A  pdb=" N   GLY A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 6.527A  pdb=" N   ALA A 232 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 305
    Processing helix  chain 'A' and resid 307 through 317
      removed outlier: 3.523A  pdb=" N   ALA A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 317 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 340 through 368
      removed outlier: 3.628A  pdb=" N   ILE A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 393
      removed outlier: 3.583A  pdb=" N   THR A 372 " --> pdb=" O   GLY A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 484
      removed outlier: 3.550A  pdb=" N   VAL A 484 " --> pdb=" O   LEU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 489
    Processing helix  chain 'A' and resid 490 through 514
      removed outlier: 3.919A  pdb=" N   ALA A 514 " --> pdb=" O   MET A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 544
    Processing helix  chain 'C' and resid 141 through 147
    Processing helix  chain 'C' and resid 202 through 208
    Processing helix  chain 'D' and resid 47 through 51
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.570A  pdb=" N   GLN D  84 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   GLY D  85 " --> pdb=" O   LYS D  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 81 through 85'
    Processing helix  chain 'D' and resid 106 through 110
      removed outlier: 3.876A  pdb=" N   THR D 110 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 183
      removed outlier: 3.653A  pdb=" N   GLY D 182 " --> pdb=" O   TRP D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 213
    Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.683A  pdb=" N   ASP C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33
      removed outlier: 6.697A  pdb=" N   MET C  31 " --> pdb=" O   GLU C 125 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ILE C  68 " --> pdb=" O   TRP C  55 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   GLN C  57 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   LEU C  66 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 137 through 138
      removed outlier: 3.567A  pdb=" N   VAL C 153 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   SER C 151 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   LEU C 201 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   VAL C 153 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   LEU C 199 " --> pdb=" O   VAL C 153 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   PHE C 155 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   SER C 197 " --> pdb=" O   PHE C 155 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ASN C 157 " --> pdb=" O   MET C 195 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   MET C 195 " --> pdb=" O   ASN C 157 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170
      removed outlier: 3.512A  pdb=" N   CYS C 214 " --> pdb=" O   LYS C 227 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE C 225 " --> pdb=" O   ALA C 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25
      removed outlier: 3.812A  pdb=" N   VAL D  37 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU D 102 " --> pdb=" O   VAL D  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.636A  pdb=" N   MET D  53 " --> pdb=" O   TRP D  69 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP D  69 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   TRP D  55 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 146
      removed outlier: 4.951A  pdb=" N   GLY D 164 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL D 206 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LEU D 166 " --> pdb=" O   SER D 204 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   SER D 204 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   LYS D 168 " --> pdb=" O   LEU D 202 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU D 202 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146
      removed outlier: 4.951A  pdb=" N   GLY D 164 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL D 206 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LEU D 166 " --> pdb=" O   SER D 204 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   SER D 204 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   LYS D 168 " --> pdb=" O   LEU D 202 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU D 202 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 219 through 222

    414 hydrogen bonds defined for protein.
    1165 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: 1.02

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1254
        1.33 -     1.45: 1461
        1.45 -     1.57: 3512
        1.57 -     1.69: 0
        1.69 -     1.82: 55
  Bond restraints: 6282
  Sorted by residual:
  bond pdb=" C   LEU A 213 "
       pdb=" O   LEU A 213 "
    ideal  model  delta    sigma   weight residual
    1.236  1.303 -0.066 1.15e-02 7.56e+03 3.34e+01
  bond pdb=" C   ALA A 379 "
       pdb=" O   ALA A 379 "
    ideal  model  delta    sigma   weight residual
    1.236  1.298 -0.061 1.15e-02 7.56e+03 2.85e+01
  bond pdb=" C   SER A 382 "
       pdb=" O   SER A 382 "
    ideal  model  delta    sigma   weight residual
    1.236  1.297 -0.061 1.15e-02 7.56e+03 2.78e+01
  bond pdb=" C   ASP A 166 "
       pdb=" O   ASP A 166 "
    ideal  model  delta    sigma   weight residual
    1.235  1.294 -0.058 1.22e-02 6.72e+03 2.28e+01
  bond pdb=" C   CYS A 217 "
       pdb=" O   CYS A 217 "
    ideal  model  delta    sigma   weight residual
    1.236  1.289 -0.053 1.15e-02 7.56e+03 2.14e+01
  ... (remaining 6277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 8185
        2.46 -     4.91: 346
        4.91 -     7.37: 29
        7.37 -     9.82: 6
        9.82 -    12.28: 3
  Bond angle restraints: 8569
  Sorted by residual:
  angle pdb=" N   PRO A 397 "
        pdb=" CA  PRO A 397 "
        pdb=" C   PRO A 397 "
      ideal   model   delta    sigma   weight residual
     113.47  101.19   12.28 1.43e+00 4.89e-01 7.37e+01
  angle pdb=" N   PRO D 192 "
        pdb=" CA  PRO D 192 "
        pdb=" CB  PRO D 192 "
      ideal   model   delta    sigma   weight residual
     103.31  110.26   -6.95 8.90e-01 1.26e+00 6.11e+01
  angle pdb=" N   PRO D 148 "
        pdb=" CA  PRO D 148 "
        pdb=" CB  PRO D 148 "
      ideal   model   delta    sigma   weight residual
     103.25  111.41   -8.16 1.05e+00 9.07e-01 6.04e+01
  angle pdb=" N   PRO D 174 "
        pdb=" CA  PRO D 174 "
        pdb=" CB  PRO D 174 "
      ideal   model   delta    sigma   weight residual
     103.25  111.13   -7.88 1.05e+00 9.07e-01 5.64e+01
  angle pdb=" N   PRO D 151 "
        pdb=" CA  PRO D 151 "
        pdb=" CB  PRO D 151 "
      ideal   model   delta    sigma   weight residual
     103.25  110.81   -7.56 1.05e+00 9.07e-01 5.19e+01
  ... (remaining 8564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 3291
       17.11 -    34.22: 269
       34.22 -    51.33: 73
       51.33 -    68.44: 19
       68.44 -    85.55: 5
  Dihedral angle restraints: 3657
    sinusoidal: 1157
      harmonic: 2500
  Sorted by residual:
  dihedral pdb=" CB  CYS A 367 "
           pdb=" SG  CYS A 367 "
           pdb=" SG  CYS A 553 "
           pdb=" CB  CYS A 553 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.53  -55.53     1      1.00e+01 1.00e-02 4.17e+01
  dihedral pdb=" CA  ASP C 102 "
           pdb=" CB  ASP C 102 "
           pdb=" CG  ASP C 102 "
           pdb=" OD1 ASP C 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.93   59.93     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CA  GLU D 108 "
           pdb=" C   GLU D 108 "
           pdb=" N   ASP D 109 "
           pdb=" CA  ASP D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.09  -15.91     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 652
       0.047 -    0.093: 209
       0.093 -    0.139: 123
       0.139 -    0.185: 27
       0.185 -    0.232: 14
  Chirality restraints: 1025
  Sorted by residual:
  chirality pdb=" CA  PRO D 225 "
            pdb=" N   PRO D 225 "
            pdb=" C   PRO D 225 "
            pdb=" CB  PRO D 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  VAL A 192 "
            pdb=" N   VAL A 192 "
            pdb=" C   VAL A 192 "
            pdb=" CB  VAL A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE A 385 "
            pdb=" CA  ILE A 385 "
            pdb=" CG1 ILE A 385 "
            pdb=" CG2 ILE A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1022 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  86 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.19e+00
        pdb=" C   ASN A  86 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ASN A  86 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA A  87 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 165 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.23e+00
        pdb=" C   GLU A 165 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLU A 165 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP A 166 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 515 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   PRO A 515 "    0.039 2.00e-02 2.50e+03
        pdb=" O   PRO A 515 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A 516 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 232
        2.71 -     3.26: 6318
        3.26 -     3.81: 9660
        3.81 -     4.35: 10689
        4.35 -     4.90: 19124
  Nonbonded interactions: 46023
  Sorted by model distance:
  nonbonded pdb=" N   GLU C 101 "
            pdb=" OE1 GLU C 101 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" N   ALA C 131 "
            pdb=" CB  TYR C 160 "
     model   vdw
     2.175 3.520
  nonbonded pdb=" OD1 ASN A 100 "
            pdb="CA    CA A 601 "
     model   vdw
     2.220 2.510
  nonbonded pdb=" O   SER D  26 "
            pdb=" OG1 THR D 133 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OE1 GLU A 165 "
            pdb=" OH  TYR D  51 "
     model   vdw
     2.311 3.040
  ... (remaining 46018 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.29 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  Set stop_for_unknowns flag:              0.010
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.310
  Find NCS groups from input model:        0.030
  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:8.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
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   0.066   6285  Z= 0.608
  Angle     :  1.089  12.276   8575  Z= 0.787
  Chirality :  0.063   0.232   1025
  Planarity :  0.004   0.042   1088
  Dihedral  : 14.534  85.547   2050
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  :  6.94 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.93 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.55 (0.28), residues: 867
  helix:  0.61 (0.25), residues: 393
  sheet: -0.13 (0.39), residues: 185
  loop : -1.81 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  59 
 TYR   0.012   0.001   TYR D  51 
 PHE   0.014   0.002   PHE C  91 
 TRP   0.015   0.002   TRP A 127 
 HIS   0.004   0.001   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00808 /  0.61 ( 6282)
  covalent geometry    : angle       1.08887 /  0.79 ( 8569)
  SS BOND              : bond        0.00295 /  0.16 (    3)
  SS BOND              : angle       1.28008 /  0.74 (    6)
  hydrogen bonds       : bond        0.14583 / 10.09 (  410)
  hydrogen bonds       : angle       6.59621 /  5.05 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9258 (mm)
REVERT: A  112 MET cc_start: 0.8870 (ttt) cc_final: 0.8648 (tmm)
  outliers start: 18
  outliers final: 5
  residues processed: 54
  average time/residue: 0.5608
  time to fit residues: 31.8231
Evaluate side-chains
  40 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  553 CYS
Chi-restraints excluded: chain D residue  106 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:   40.0000
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 ASN
A 516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.068244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.049641 restraints weight = 74168.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 5.96
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6285  Z= 0.180
  Angle     :  0.647   8.275   8575  Z= 0.341
  Chirality :  0.044   0.147   1025
  Planarity :  0.005   0.055   1088
  Dihedral  :  5.453  58.795    934
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  5.44 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.18 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.84 (0.29), residues: 867
  helix:  2.22 (0.25), residues: 390
  sheet:  0.49 (0.40), residues: 179
  loop : -1.74 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.011   0.001   TYR A 538 
 PHE   0.012   0.001   PHE C  91 
 TRP   0.029   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.18 ( 6282)
  covalent geometry    : angle       0.64580 /  0.34 ( 8569)
  SS BOND              : bond        0.00286 /  0.15 (    3)
  SS BOND              : angle       1.46600 /  0.78 (    6)
  hydrogen bonds       : bond        0.06595 /  4.45 (  410)
  hydrogen bonds       : angle       4.80048 /  3.74 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 35
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 6
  residues processed: 48
  average time/residue: 0.4667
  time to fit residues: 23.7715
Evaluate side-chains
  37 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain C residue   57 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 6 optimal weight:    0.7980
   chunk 84 optimal weight:   20.0000
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0770
   chunk 55 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7542

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.071822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.053334 restraints weight = 87603.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 6.53
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6285  Z= 0.111
  Angle     :  0.565   9.074   8575  Z= 0.289
  Chirality :  0.041   0.147   1025
  Planarity :  0.004   0.049   1088
  Dihedral  :  5.031  59.338    932
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.21 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.65 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.63 (0.30), residues: 867
  helix:  3.08 (0.25), residues: 386
  sheet:  0.64 (0.40), residues: 184
  loop : -1.48 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.007   0.001   TYR C 111 
 PHE   0.009   0.001   PHE C  91 
 TRP   0.016   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.11 ( 6282)
  covalent geometry    : angle       0.56404 /  0.29 ( 8569)
  SS BOND              : bond        0.00328 /  0.17 (    3)
  SS BOND              : angle       1.28739 /  0.62 (    6)
  hydrogen bonds       : bond        0.04316 /  2.90 (  410)
  hydrogen bonds       : angle       4.30050 /  3.33 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7952 (mm-30)
  outliers start: 21
  outliers final: 5
  residues processed: 59
  average time/residue: 0.4876
  time to fit residues: 30.2481
Evaluate side-chains
  41 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  498 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 62 optimal weight:   20.0000
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.070258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.052635 restraints weight = 42214.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 4.66
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6285  Z= 0.122
  Angle     :  0.585   9.257   8575  Z= 0.293
  Chirality :  0.041   0.157   1025
  Planarity :  0.004   0.044   1088
  Dihedral  :  4.573  59.919    930
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.98 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.26 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.88 (0.30), residues: 867
  helix:  3.20 (0.25), residues: 389
  sheet:  0.86 (0.41), residues: 184
  loop : -1.33 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  59 
 TYR   0.010   0.001   TYR A 501 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.013   0.001   TRP A 127 
 HIS   0.001   0.000   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 6282)
  covalent geometry    : angle       0.58419 /  0.29 ( 8569)
  SS BOND              : bond        0.00308 /  0.16 (    3)
  SS BOND              : angle       1.04747 /  0.55 (    6)
  hydrogen bonds       : bond        0.04822 /  3.25 (  410)
  hydrogen bonds       : angle       4.23683 /  3.28 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: C   51 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9316 (m)
REVERT: D   29 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7821 (mm-30)
  outliers start: 16
  outliers final: 5
  residues processed: 52
  average time/residue: 0.5233
  time to fit residues: 28.6948
Evaluate side-chains
  42 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 60 optimal weight:   40.0000
   chunk 82 optimal weight:   30.0000
   chunk 41 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 57 optimal weight:   50.0000
   chunk 31 optimal weight:    5.9990
   overall best weight:    5.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.064014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.045294 restraints weight = 81504.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 6.08
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   6285  Z= 0.304
  Angle     :  0.721   9.323   8575  Z= 0.379
  Chirality :  0.045   0.163   1025
  Planarity :  0.005   0.053   1088
  Dihedral  :  4.870  59.391    930
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.48 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.97 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.58 (0.30), residues: 867
  helix:  2.77 (0.25), residues: 383
  sheet:  0.86 (0.40), residues: 182
  loop : -1.20 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  88 
 TYR   0.013   0.001   TYR D 121 
 PHE   0.010   0.001   PHE C  91 
 TRP   0.015   0.002   TRP A 224 
 HIS   0.004   0.001   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00692 /  0.30 ( 6282)
  covalent geometry    : angle       0.71992 /  0.38 ( 8569)
  SS BOND              : bond        0.00429 /  0.23 (    3)
  SS BOND              : angle       1.47706 /  0.82 (    6)
  hydrogen bonds       : bond        0.08089 /  5.46 (  410)
  hydrogen bonds       : angle       4.84783 /  3.75 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9166 (m) cc_final: 0.8900 (m)
REVERT: C   51 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9341 (m)
REVERT: D   29 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7670 (mm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 49
  average time/residue: 0.6080
  time to fit residues: 31.2714
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 75 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  57 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.067804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.049528 restraints weight = 68283.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 5.66
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6285  Z= 0.151
  Angle     :  0.614   8.560   8575  Z= 0.313
  Chirality :  0.041   0.153   1025
  Planarity :  0.004   0.049   1088
  Dihedral  :  4.648  58.325    930
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 24.69 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.89 (0.30), residues: 867
  helix:  3.05 (0.25), residues: 388
  sheet:  1.04 (0.41), residues: 177
  loop : -1.14 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  59 
 TYR   0.009   0.001   TYR A 538 
 PHE   0.008   0.001   PHE A 360 
 TRP   0.010   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 6282)
  covalent geometry    : angle       0.61051 /  0.31 ( 8569)
  SS BOND              : bond        0.00392 /  0.21 (    3)
  SS BOND              : angle       2.48999 /  1.21 (    6)
  hydrogen bonds       : bond        0.05706 /  3.85 (  410)
  hydrogen bonds       : angle       4.37035 /  3.37 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  132 CYS cc_start: 0.9172 (m) cc_final: 0.8825 (m)
REVERT: C   51 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9303 (m)
REVERT: D   29 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7827 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 51
  average time/residue: 0.5690
  time to fit residues: 30.5798
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue  105 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 85 optimal weight:   40.0000
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 79 optimal weight:   50.0000
   overall best weight:    1.7788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.067098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.049252 restraints weight = 50802.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 5.07
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6285  Z= 0.146
  Angle     :  0.641  10.415   8575  Z= 0.323
  Chirality :  0.042   0.165   1025
  Planarity :  0.004   0.055   1088
  Dihedral  :  4.165  49.588    927
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.56 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.97 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.91 (0.30), residues: 867
  helix:  3.01 (0.25), residues: 389
  sheet:  1.02 (0.41), residues: 179
  loop : -1.06 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  40 
 TYR   0.008   0.001   TYR A 538 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.009   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 6282)
  covalent geometry    : angle       0.63768 /  0.32 ( 8569)
  SS BOND              : bond        0.00360 /  0.19 (    3)
  SS BOND              : angle       2.41429 /  1.18 (    6)
  hydrogen bonds       : bond        0.05524 /  3.73 (  410)
  hydrogen bonds       : angle       4.28184 /  3.30 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8822 (mtp) cc_final: 0.8318 (mmm)
REVERT: A  132 CYS cc_start: 0.9163 (m) cc_final: 0.8917 (m)
REVERT: D   29 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7894 (mm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 50
  average time/residue: 0.5233
  time to fit residues: 27.6131
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 59 optimal weight:   50.0000
   chunk 60 optimal weight:   40.0000
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   overall best weight:    2.5788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.065913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.047797 restraints weight = 55971.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 5.27
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
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      :  0.004   0.040   6285  Z= 0.178
  Angle     :  0.654  11.548   8575  Z= 0.336
  Chirality :  0.042   0.160   1025
  Planarity :  0.004   0.051   1088
  Dihedral  :  4.214  48.820    927
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.15 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.93 (0.30), residues: 867
  helix:  3.00 (0.25), residues: 384
  sheet:  1.13 (0.40), residues: 177
  loop : -0.99 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.010   0.001   TYR A 538 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.010   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 6282)
  covalent geometry    : angle       0.65158 /  0.33 ( 8569)
  SS BOND              : bond        0.00377 /  0.20 (    3)
  SS BOND              : angle       2.38744 /  1.17 (    6)
  hydrogen bonds       : bond        0.06111 /  4.13 (  410)
  hydrogen bonds       : angle       4.36471 /  3.36 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9155 (m) cc_final: 0.8916 (m)
REVERT: D   29 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7791 (mm-30)
REVERT: D   59 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8732 (tpp80)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.5962
  time to fit residues: 31.9152
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue   59 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.067715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.049590 restraints weight = 75101.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 6.07
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6285  Z= 0.136
  Angle     :  0.653  12.826   8575  Z= 0.329
  Chirality :  0.041   0.171   1025
  Planarity :  0.004   0.054   1088
  Dihedral  :  4.115  47.966    927
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.21 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.51 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.03 (0.30), residues: 867
  helix:  3.06 (0.25), residues: 389
  sheet:  1.26 (0.40), residues: 177
  loop : -1.02 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.008   0.001   TYR C 111 
 PHE   0.008   0.001   PHE A 295 
 TRP   0.009   0.001   TRP D  69 
 HIS   0.002   0.000   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 6282)
  covalent geometry    : angle       0.65063 /  0.33 ( 8569)
  SS BOND              : bond        0.00360 /  0.19 (    3)
  SS BOND              : angle       2.30219 /  1.12 (    6)
  hydrogen bonds       : bond        0.05073 /  3.42 (  410)
  hydrogen bonds       : angle       4.20717 /  3.24 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8773 (mtp) cc_final: 0.8433 (mpp)
REVERT: D   29 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7825 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 0.6060
  time to fit residues: 31.1376
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 17 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0870
   chunk 23 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0050
   chunk 24 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.7572

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.070570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.052491 restraints weight = 77399.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 6.33
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6285  Z= 0.121
  Angle     :  0.652  12.665   8575  Z= 0.326
  Chirality :  0.041   0.160   1025
  Planarity :  0.004   0.051   1088
  Dihedral  :  4.022  46.639    927
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.28 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.87 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.05 (0.30), residues: 867
  helix:  3.14 (0.25), residues: 389
  sheet:  1.16 (0.40), residues: 185
  loop : -1.09 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  40 
 TYR   0.008   0.001   TYR C 111 
 PHE   0.009   0.001   PHE A 360 
 TRP   0.011   0.001   TRP D  69 
 HIS   0.002   0.000   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 6282)
  covalent geometry    : angle       0.64937 /  0.32 ( 8569)
  SS BOND              : bond        0.00325 /  0.17 (    3)
  SS BOND              : angle       2.20110 /  1.07 (    6)
  hydrogen bonds       : bond        0.04362 /  2.93 (  410)
  hydrogen bonds       : angle       4.13532 /  3.18 ( 1165)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: C  127 LYS cc_start: 0.9391 (mmmm) cc_final: 0.9152 (mmmm)
REVERT: D   29 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7755 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 54
  average time/residue: 0.5299
  time to fit residues: 30.1579
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.0060
   chunk 84 optimal weight:    0.0470
   chunk 37 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 83 optimal weight:   50.0000
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6156

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.053275 restraints weight = 74654.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 6.28
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6285  Z= 0.122
  Angle     :  0.676  12.591   8575  Z= 0.332
  Chirality :  0.041   0.172   1025
  Planarity :  0.004   0.052   1088
  Dihedral  :  3.956  46.463    927
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.63 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.04 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  2.09 (0.30), residues: 867
  helix:  3.13 (0.25), residues: 389
  sheet:  1.26 (0.41), residues: 179
  loop : -1.04 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  40 
 TYR   0.007   0.001   TYR C 111 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.011   0.001   TRP D  69 
 HIS   0.001   0.000   HIS A 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 6282)
  covalent geometry    : angle       0.67382 /  0.33 ( 8569)
  SS BOND              : bond        0.00334 /  0.18 (    3)
  SS BOND              : angle       2.16848 /  1.05 (    6)
  hydrogen bonds       : bond        0.04264 /  2.85 (  410)
  hydrogen bonds       : angle       4.07953 /  3.15 ( 1165)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1569.56 seconds
wall clock time: 27 minutes 33.02 seconds (1653.02 seconds total)