Starting phenix.real_space_refine
on Sat May 10 11:44:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dl6_27497/05_2025/8dl6_27497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl6_27497/05_2025/8dl6_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dl6_27497/05_2025/8dl6_27497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl6_27497/05_2025/8dl6_27497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl6_27497/05_2025/8dl6_27497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl6_27497/05_2025/8dl6_27497.cif"
  }
  resolution = 3.0
  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=   0.014 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3}
          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: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 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: 7.65, per 1000 atoms: 1.24
  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: 1.61
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.68
  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: 1.73

  Time building geometry restraints manager: 1.87 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:             0.580
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     22.340
  Find NCS groups from input model:        0.070
  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:11.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
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 (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: -0.55 (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
 TRP   0.015   0.002   TRP A 127 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.014   0.002   PHE C  91 
 TYR   0.012   0.001   TYR D  51 
 ARG   0.005   0.001   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14583 (  410)
  hydrogen bonds       : angle       6.59621 ( 1165)
  SS BOND              : bond        0.00295 (    3)
  SS BOND              : angle       1.28008 (    6)
  covalent geometry    : bond        0.00808 ( 6282)
  covalent geometry    : angle       1.08887 ( 8569)

*********************** 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  : 0.647 
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: 0.8639 (tmm)
  outliers start: 18
  outliers final: 5
  residues processed: 54
  average time/residue: 1.1166
  time to fit residues: 63.8113
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  : 0.671 
-------------------------------------------------------------------------------
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 72 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    8.9990
   chunk 78 optimal weight:   30.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3440 r_free = 0.3440 target = 0.067768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.048982 restraints weight = 93234.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 6.56
r_work: 0.2665 rms_B_bonded: 6.47 restraints_weight: 2.0000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6285  Z= 0.200
  Angle     :  0.656   8.034   8575  Z= 0.348
  Chirality :  0.044   0.150   1025
  Planarity :  0.005   0.056   1088
  Dihedral  :  5.481  58.514    934
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  5.21 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.82 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.81 (0.29), residues: 867
  helix:  2.17 (0.25), residues: 390
  sheet:  0.48 (0.40), residues: 179
  loop : -1.74 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.012   0.001   PHE C  91 
 TYR   0.012   0.001   TYR A 538 
 ARG   0.004   0.001   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06872 (  410)
  hydrogen bonds       : angle       4.85948 ( 1165)
  SS BOND              : bond        0.00300 (    3)
  SS BOND              : angle       1.56620 (    6)
  covalent geometry    : bond        0.00445 ( 6282)
  covalent geometry    : angle       0.65480 ( 8569)

*********************** 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: 19
    poor density    : 34
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 7
  residues processed: 48
  average time/residue: 1.0788
  time to fit residues: 55.1546
Evaluate side-chains
  38 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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 A residue  385 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 49 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:   40.0000
   chunk 76 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3463 r_free = 0.3463 target = 0.068960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.050937 restraints weight = 50199.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 5.03
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6285  Z= 0.139
  Angle     :  0.583   8.823   8575  Z= 0.305
  Chirality :  0.042   0.146   1025
  Planarity :  0.004   0.046   1088
  Dihedral  :  5.113  58.741    932
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.79 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.00 %
    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 (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:  1.47 (0.30), residues: 867
  helix:  2.89 (0.25), residues: 386
  sheet:  0.61 (0.40), residues: 183
  loop : -1.49 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.008   0.001   TYR A 538 
 ARG   0.002   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05559 (  410)
  hydrogen bonds       : angle       4.46621 ( 1165)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       1.34081 (    6)
  covalent geometry    : bond        0.00294 ( 6282)
  covalent geometry    : angle       0.58246 ( 8569)

*********************** 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
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7690 (mm-30)
  outliers start: 19
  outliers final: 5
  residues processed: 53
  average time/residue: 1.2309
  time to fit residues: 68.9891
Evaluate side-chains
  38 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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 13 optimal weight:    0.0980
   chunk 45 optimal weight:    0.5980
   chunk 62 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   overall best weight:    1.1120

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3488 r_free = 0.3488 target = 0.070249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.052646 restraints weight = 41266.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 4.59
r_work (final): 0.2950
-------------------------------------------------------------------------------
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 = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6285  Z= 0.118
  Angle     :  0.570   8.612   8575  Z= 0.290
  Chirality :  0.041   0.155   1025
  Planarity :  0.004   0.044   1088
  Dihedral  :  4.594  59.669    930
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.43 %
    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 (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:  1.81 (0.30), residues: 867
  helix:  3.19 (0.25), residues: 386
  sheet:  0.80 (0.41), residues: 184
  loop : -1.38 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 127 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.007   0.001   TYR C 111 
 ARG   0.005   0.000   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  410)
  hydrogen bonds       : angle       4.23518 ( 1165)
  SS BOND              : bond        0.00326 (    3)
  SS BOND              : angle       1.11005 (    6)
  covalent geometry    : bond        0.00243 ( 6282)
  covalent geometry    : angle       0.56974 ( 8569)

*********************** 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
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9177 (m) cc_final: 0.8835 (m)
REVERT: C   51 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9302 (m)
REVERT: D   29 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7904 (mm-30)
  outliers start: 18
  outliers final: 7
  residues processed: 55
  average time/residue: 1.0402
  time to fit residues: 60.8552
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  : 0.636 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
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 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 67 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3434 r_free = 0.3434 target = 0.067738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.049310 restraints weight = 83620.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 6.22
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6285  Z= 0.175
  Angle     :  0.614   9.316   8575  Z= 0.317
  Chirality :  0.042   0.161   1025
  Planarity :  0.004   0.048   1088
  Dihedral  :  4.650  59.924    930
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.67 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.08 %
    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 (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:  1.78 (0.30), residues: 867
  helix:  2.97 (0.25), residues: 389
  sheet:  0.91 (0.41), residues: 179
  loop : -1.20 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.010   0.001   TYR A 538 
 ARG   0.003   0.000   ARG A  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06114 (  410)
  hydrogen bonds       : angle       4.39487 ( 1165)
  SS BOND              : bond        0.00375 (    3)
  SS BOND              : angle       1.21438 (    6)
  covalent geometry    : bond        0.00388 ( 6282)
  covalent geometry    : angle       0.61385 ( 8569)

*********************** 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
  57 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9151 (m) cc_final: 0.8907 (m)
REVERT: C   51 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9312 (m)
REVERT: D   29 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7855 (mm-30)
  outliers start: 18
  outliers final: 8
  residues processed: 54
  average time/residue: 1.1982
  time to fit residues: 68.3683
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  136 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
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 2 optimal weight:    7.9990
   chunk 55 optimal weight:   50.0000
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:   20.0000
   chunk 83 optimal weight:   40.0000
   chunk 70 optimal weight:    0.8980
   chunk 57 optimal weight:   40.0000
   chunk 63 optimal weight:   30.0000
   chunk 68 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3449 r_free = 0.3449 target = 0.069028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.051713 restraints weight = 62979.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 5.29
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6285  Z= 0.151
  Angle     :  0.610   8.761   8575  Z= 0.309
  Chirality :  0.041   0.158   1025
  Planarity :  0.004   0.050   1088
  Dihedral  :  4.596  58.847    930
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 24.15 %
    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 (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:  1.91 (0.30), residues: 867
  helix:  3.10 (0.25), residues: 386
  sheet:  0.95 (0.41), residues: 179
  loop : -1.11 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.008   0.001   PHE A 360 
 TYR   0.009   0.001   TYR A 538 
 ARG   0.002   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05594 (  410)
  hydrogen bonds       : angle       4.29573 ( 1165)
  SS BOND              : bond        0.00363 (    3)
  SS BOND              : angle       1.13088 (    6)
  covalent geometry    : bond        0.00333 ( 6282)
  covalent geometry    : angle       0.60904 ( 8569)

*********************** 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
  55 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9164 (m) cc_final: 0.8896 (m)
REVERT: C   51 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9325 (m)
REVERT: D   29 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7859 (mm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 53
  average time/residue: 1.1232
  time to fit residues: 63.0068
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
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 A residue  553 CYS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:   50.0000
   chunk 56 optimal weight:   50.0000
   chunk 85 optimal weight:   30.0000
   chunk 59 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:   30.0000
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0470
   chunk 53 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.8086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.066842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.049057 restraints weight = 53034.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 5.06
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6285  Z= 0.189
  Angle     :  0.661  10.046   8575  Z= 0.339
  Chirality :  0.042   0.166   1025
  Planarity :  0.004   0.054   1088
  Dihedral  :  4.622  57.535    930
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  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 (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:  1.83 (0.30), residues: 867
  helix:  2.95 (0.25), residues: 388
  sheet:  0.98 (0.41), residues: 179
  loop : -1.09 (0.38), residues: 300

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06433 (  410)
  hydrogen bonds       : angle       4.41656 ( 1165)
  SS BOND              : bond        0.00387 (    3)
  SS BOND              : angle       1.23497 (    6)
  covalent geometry    : bond        0.00426 ( 6282)
  covalent geometry    : angle       0.65993 ( 8569)

*********************** 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
  55 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9138 (m) cc_final: 0.8816 (m)
REVERT: C   51 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9334 (m)
REVERT: D   29 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7782 (mm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 53
  average time/residue: 1.2012
  time to fit residues: 67.2029
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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 A residue  553 CYS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   57 GLN
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 18 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 78 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 82 optimal weight:   40.0000
   chunk 79 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   overall best weight:    3.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.064515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.046156 restraints weight = 61668.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 5.48
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6285  Z= 0.236
  Angle     :  0.700  10.781   8575  Z= 0.362
  Chirality :  0.043   0.161   1025
  Planarity :  0.004   0.051   1088
  Dihedral  :  4.344  48.309    927
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.90 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.79 %
    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 (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:  1.74 (0.30), residues: 867
  helix:  2.81 (0.25), residues: 387
  sheet:  1.02 (0.39), residues: 183
  loop : -1.10 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A 118 
 PHE   0.007   0.001   PHE A 295 
 TYR   0.012   0.001   TYR A 501 
 ARG   0.002   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07151 (  410)
  hydrogen bonds       : angle       4.60447 ( 1165)
  SS BOND              : bond        0.00426 (    3)
  SS BOND              : angle       1.33892 (    6)
  covalent geometry    : bond        0.00536 ( 6282)
  covalent geometry    : angle       0.69922 ( 8569)

*********************** 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
  57 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9119 (m) cc_final: 0.8880 (m)
REVERT: D   29 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: D   65 GLU cc_start: 0.8608 (mt-10) cc_final: 0.7963 (mp0)
  outliers start: 16
  outliers final: 7
  residues processed: 56
  average time/residue: 1.2279
  time to fit residues: 72.5071
Evaluate side-chains
  44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 81 optimal weight:   40.0000
   chunk 12 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.069047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.050573 restraints weight = 94858.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 6.75
r_work: 0.2756 rms_B_bonded: 6.70 restraints_weight: 2.0000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6285  Z= 0.126
  Angle     :  0.668  12.873   8575  Z= 0.333
  Chirality :  0.041   0.179   1025
  Planarity :  0.004   0.055   1088
  Dihedral  :  4.102  46.833    927
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.63 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 24.87 %
    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 (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:  1.98 (0.30), residues: 867
  helix:  3.15 (0.26), residues: 382
  sheet:  1.12 (0.40), residues: 185
  loop : -1.13 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  69 
 HIS   0.001   0.000   HIS A 535 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.008   0.001   TYR A 501 
 ARG   0.004   0.000   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04531 (  410)
  hydrogen bonds       : angle       4.16282 ( 1165)
  SS BOND              : bond        0.00346 (    3)
  SS BOND              : angle       2.29551 (    6)
  covalent geometry    : bond        0.00270 ( 6282)
  covalent geometry    : angle       0.66529 ( 8569)

*********************** 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
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: C  127 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9139 (mmmm)
REVERT: D   29 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8086 (mm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 56
  average time/residue: 1.2011
  time to fit residues: 70.9690
Evaluate side-chains
  47 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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 C residue   23 VAL
Chi-restraints excluded: chain C residue   57 GLN
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 2 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 49 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 85 optimal weight:   50.0000
   chunk 72 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    8.9990
   overall best weight:    2.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.067593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.048964 restraints weight = 89712.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 6.60
r_work: 0.2706 rms_B_bonded: 6.56 restraints_weight: 2.0000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2958

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= 0.157
  Angle     :  0.680  13.154   8575  Z= 0.344
  Chirality :  0.042   0.199   1025
  Planarity :  0.004   0.054   1088
  Dihedral  :  4.117  46.656    927
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.32 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.22 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.97 (0.30), residues: 867
  helix:  3.05 (0.25), residues: 386
  sheet:  1.12 (0.40), residues: 179
  loop : -1.02 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  37 
 HIS   0.002   0.000   HIS A  32 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.008   0.001   TYR C 111 
 ARG   0.004   0.000   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05369 (  410)
  hydrogen bonds       : angle       4.27585 ( 1165)
  SS BOND              : bond        0.00369 (    3)
  SS BOND              : angle       2.34005 (    6)
  covalent geometry    : bond        0.00352 ( 6282)
  covalent geometry    : angle       0.67714 ( 8569)

********************** 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
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.693 
Fit side-chains
REVERT: C  127 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9186 (mmmm)
REVERT: D   29 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7990 (mm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 52
  average time/residue: 1.2063
  time to fit residues: 66.3130
Evaluate side-chains
  49 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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 C residue   23 VAL
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue  106 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 83 optimal weight:   50.0000
   chunk 64 optimal weight:   50.0000
   chunk 82 optimal weight:   20.0000
   chunk 53 optimal weight:    0.7980
   chunk 81 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    3.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.065351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.046868 restraints weight = 68584.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 5.89
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6285  Z= 0.219
  Angle     :  0.728  12.010   8575  Z= 0.374
  Chirality :  0.043   0.180   1025
  Planarity :  0.004   0.053   1088
  Dihedral  :  4.282  46.831    927
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.02 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 25.40 %
    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 (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:  1.79 (0.30), residues: 867
  helix:  2.77 (0.25), residues: 389
  sheet:  1.03 (0.40), residues: 179
  loop : -0.93 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  37 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.008   0.001   PHE A 360 
 TYR   0.011   0.001   TYR A 501 
 ARG   0.005   0.001   ARG D  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06760 (  410)
  hydrogen bonds       : angle       4.49820 ( 1165)
  SS BOND              : bond        0.00397 (    3)
  SS BOND              : angle       2.42415 (    6)
  covalent geometry    : bond        0.00498 ( 6282)
  covalent geometry    : angle       0.72497 ( 8569)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3548.70 seconds
wall clock time: 62 minutes 0.17 seconds (3720.17 seconds total)