Starting phenix.real_space_refine
on Tue Feb 11 15:39:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dl6_27497/02_2025/8dl6_27497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl6_27497/02_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_27497/02_2025/8dl6_27497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl6_27497/02_2025/8dl6_27497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl6_27497/02_2025/8dl6_27497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl6_27497/02_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-5592/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: 5.29, per 1000 atoms: 0.86
  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: 1.58
  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: 1.02
  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: 1.82

  Time building geometry restraints manager: 1.83 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:             0.540
  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:                     20.220
  Find NCS groups from input model:        0.080
  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:10.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.000
-------------------------------------------------------------------------------
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   6282  Z= 0.523
  Angle     :  1.089  12.276   8569  Z= 0.788
  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 

*********************** 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  : 0.708 
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: 1.2094
  time to fit residues: 69.1832
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  : 0.831 
-------------------------------------------------------------------------------
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:    5.9990
   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:    3.1988

-------------------------------------------------------------------------------
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 = 0.3434 r_free = 0.3434 target = 0.067462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.048629 restraints weight = 93381.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 6.54
r_work: 0.2657 rms_B_bonded: 6.44 restraints_weight: 2.0000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    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 = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6282  Z= 0.314
  Angle     :  0.661   8.126   8569  Z= 0.350
  Chirality :  0.044   0.152   1025
  Planarity :  0.005   0.056   1088
  Dihedral  :  5.500  58.905    934
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  5.32 %
    Favored  : 94.21 %
  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:  0.82 (0.29), residues: 867
  helix:  2.19 (0.25), residues: 388
  sheet:  0.49 (0.40), residues: 179
  loop : -1.72 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 127 
 HIS   0.004   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 

*********************** 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
  52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 33
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 7
  residues processed: 47
  average time/residue: 1.1513
  time to fit residues: 57.5799
Evaluate side-chains
  37 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 60 optimal weight:   40.0000
   chunk 76 optimal weight:    7.9990
   chunk 63 optimal weight:   50.0000
   chunk 57 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.064637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.046257 restraints weight = 51312.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2795 rms_B_bonded: 5.07
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2794
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6282  Z= 0.388
  Angle     :  0.666   8.302   8569  Z= 0.357
  Chirality :  0.044   0.164   1025
  Planarity :  0.005   0.045   1088
  Dihedral  :  5.256  57.713    932
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.71 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.72 %
    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:  1.17 (0.29), residues: 867
  helix:  2.47 (0.25), residues: 388
  sheet:  0.61 (0.40), residues: 181
  loop : -1.52 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 127 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.011   0.001   PHE C  91 
 TYR   0.012   0.001   TYR D 121 
 ARG   0.003   0.001   ARG A  40 

*********************** 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
  54 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 34
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9173 (m) cc_final: 0.8923 (m)
REVERT: D   29 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7765 (mm-30)
  outliers start: 20
  outliers final: 7
  residues processed: 48
  average time/residue: 1.2728
  time to fit residues: 64.4575
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  : 0.742 
-------------------------------------------------------------------------------
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  378 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain C residue   57 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 82 optimal weight:   30.0000
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.069259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.051563 restraints weight = 41225.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 4.59
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6282  Z= 0.159
  Angle     :  0.576   9.339   8569  Z= 0.296
  Chirality :  0.041   0.156   1025
  Planarity :  0.004   0.045   1088
  Dihedral  :  4.995  58.100    932
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.75 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.43 %
    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:  1.68 (0.30), residues: 867
  helix:  3.02 (0.25), residues: 387
  sheet:  0.76 (0.40), residues: 184
  loop : -1.38 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 127 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.008   0.001   TYR A 501 
 ARG   0.004   0.000   ARG D  59 

*********************** 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
  62 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9180 (m) cc_final: 0.8816 (m)
REVERT: C   51 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9301 (m)
REVERT: D   29 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7697 (mm-30)
  outliers start: 20
  outliers final: 6
  residues processed: 59
  average time/residue: 1.0051
  time to fit residues: 63.0930
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  : 0.674 
-------------------------------------------------------------------------------
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   23 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain D residue  106 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 64 optimal weight:   50.0000
   chunk 54 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.067882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.049341 restraints weight = 84074.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 6.27
r_work: 0.2681 rms_B_bonded: 6.27 restraints_weight: 2.0000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6282  Z= 0.231
  Angle     :  0.600   8.233   8569  Z= 0.308
  Chirality :  0.041   0.156   1025
  Planarity :  0.004   0.049   1088
  Dihedral  :  4.619  57.800    930
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.13 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.79 %
    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:  1.74 (0.30), residues: 867
  helix:  3.00 (0.25), residues: 387
  sheet:  0.85 (0.40), residues: 185
  loop : -1.29 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.011   0.001   TYR A 501 
 ARG   0.003   0.000   ARG D  59 

*********************** 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
  55 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9045 (m) cc_final: 0.8808 (m)
REVERT: C   51 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9320 (m)
REVERT: D   29 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8030 (mm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 52
  average time/residue: 1.1891
  time to fit residues: 65.3989
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
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  378 LEU
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   57 GLN
Chi-restraints excluded: chain D residue  106 THR
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:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 83 optimal weight:   30.0000
   chunk 70 optimal weight:    0.5980
   chunk 57 optimal weight:   40.0000
   chunk 63 optimal weight:   30.0000
   chunk 68 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.068637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.050491 restraints weight = 61016.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 5.47
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6282  Z= 0.195
  Angle     :  0.592  10.175   8569  Z= 0.301
  Chirality :  0.041   0.152   1025
  Planarity :  0.004   0.049   1088
  Dihedral  :  4.557  57.934    930
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.86 %
    Favored  : 94.79 %
  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 (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:  1.88 (0.30), residues: 867
  helix:  3.09 (0.25), residues: 387
  sheet:  1.03 (0.41), residues: 179
  loop : -1.21 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.011   0.001   TYR A 501 
 ARG   0.003   0.000   ARG A  40 

*********************** 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
  57 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9139 (m) cc_final: 0.8883 (m)
REVERT: C   51 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9280 (m)
REVERT: D   29 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7747 (mm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 55
  average time/residue: 1.2314
  time to fit residues: 71.5515
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
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  378 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  509 ILE
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 D residue  106 THR
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:    0.1980
   chunk 85 optimal weight:   40.0000
   chunk 59 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.069109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.051225 restraints weight = 52426.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 5.19
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6282  Z= 0.159
  Angle     :  0.602  10.528   8569  Z= 0.302
  Chirality :  0.041   0.164   1025
  Planarity :  0.004   0.057   1088
  Dihedral  :  4.063  47.853    927
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.98 %
    Favored  : 94.68 %
  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:  2.04 (0.30), residues: 867
  helix:  3.18 (0.25), residues: 387
  sheet:  1.19 (0.41), residues: 179
  loop : -1.14 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  69 
 HIS   0.003   0.001   HIS A 507 
 PHE   0.011   0.001   PHE A 508 
 TYR   0.009   0.001   TYR A 501 
 ARG   0.002   0.000   ARG A  40 

*********************** 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
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8802 (mtp) cc_final: 0.8436 (mpp)
REVERT: A  132 CYS cc_start: 0.9134 (m) cc_final: 0.8907 (m)
REVERT: C   51 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9266 (m)
REVERT: D   29 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7804 (mm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 58
  average time/residue: 1.1200
  time to fit residues: 68.8005
Evaluate side-chains
  49 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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  378 LEU
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 D residue  106 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    8.9990
   chunk 78 optimal weight:   30.0000
   chunk 19 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 82 optimal weight:   30.0000
   chunk 79 optimal weight:   40.0000
   chunk 11 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
C  57 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.061984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.043473 restraints weight = 62562.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 5.50
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.072   6282  Z= 0.654
  Angle     :  0.828  10.983   8569  Z= 0.437
  Chirality :  0.048   0.176   1025
  Planarity :  0.005   0.053   1088
  Dihedral  :  4.608  48.478    927
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.48 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 24.51 %
    Favored  : 72.27 %
  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:  1.40 (0.29), residues: 867
  helix:  2.29 (0.25), residues: 391
  sheet:  1.02 (0.39), residues: 187
  loop : -1.10 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 224 
 HIS   0.005   0.002   HIS A  32 
 PHE   0.012   0.002   PHE A 459 
 TYR   0.028   0.002   TYR A 501 
 ARG   0.004   0.001   ARG A  88 

*********************** 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
  54 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8839 (mtp) cc_final: 0.8525 (mpp)
REVERT: A  132 CYS cc_start: 0.9165 (m) cc_final: 0.8864 (m)
REVERT: C   57 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.9031 (tt0)
REVERT: D   29 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7826 (mm-30)
REVERT: D   59 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8822 (tpp80)
  outliers start: 18
  outliers final: 7
  residues processed: 53
  average time/residue: 1.3182
  time to fit residues: 74.0846
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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  391 VAL
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 D residue   59 ARG
Chi-restraints excluded: chain D residue  106 THR
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:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 81 optimal weight:   40.0000
   chunk 12 optimal weight:    0.9990
   chunk 63 optimal weight:   30.0000
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
C  57 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.068513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.050433 restraints weight = 93885.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 6.72
r_work: 0.2708 rms_B_bonded: 6.59 restraints_weight: 2.0000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6282  Z= 0.184
  Angle     :  0.657  11.931   8569  Z= 0.336
  Chirality :  0.042   0.193   1025
  Planarity :  0.004   0.052   1088
  Dihedral  :  4.222  46.308    927
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.09 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 25.76 %
    Favored  : 72.63 %
  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:  1.84 (0.30), residues: 867
  helix:  2.90 (0.25), residues: 389
  sheet:  1.10 (0.40), residues: 187
  loop : -1.15 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  69 
 HIS   0.002   0.000   HIS A 507 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.012   0.001   TYR A 501 
 ARG   0.002   0.000   ARG A  40 

*********************** 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
  52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8815 (mtp) cc_final: 0.8459 (mpp)
REVERT: A  132 CYS cc_start: 0.9034 (m) cc_final: 0.8806 (m)
REVERT: D   29 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8008 (mm-30)
REVERT: D   65 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8485 (mp0)
  outliers start: 9
  outliers final: 5
  residues processed: 50
  average time/residue: 1.2790
  time to fit residues: 67.4880
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 80 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 85 optimal weight:   40.0000
   chunk 72 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.068073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.049354 restraints weight = 91073.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 6.62
r_work: 0.2720 rms_B_bonded: 6.58 restraints_weight: 2.0000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6282  Z= 0.188
  Angle     :  0.651  12.353   8569  Z= 0.328
  Chirality :  0.041   0.168   1025
  Planarity :  0.004   0.052   1088
  Dihedral  :  4.102  46.099    927
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.98 %
    Favored  : 94.68 %
  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:  1.95 (0.30), residues: 867
  helix:  2.99 (0.26), residues: 388
  sheet:  1.15 (0.41), residues: 181
  loop : -1.03 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  69 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.010   0.001   TYR A 501 
 ARG   0.002   0.000   ARG A  40 

********************** 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
  49 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A  123 MET cc_start: 0.8796 (mtp) cc_final: 0.8426 (mpp)
REVERT: D   29 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8026 (mm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 47
  average time/residue: 1.3802
  time to fit residues: 68.2570
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 83 optimal weight:   50.0000
   chunk 64 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   chunk 53 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.067785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.049809 restraints weight = 68392.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 5.88
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6282  Z= 0.250
  Angle     :  0.679  12.417   8569  Z= 0.346
  Chirality :  0.042   0.172   1025
  Planarity :  0.004   0.052   1088
  Dihedral  :  4.129  45.835    927
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 25.76 %
    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:  1.94 (0.30), residues: 867
  helix:  2.92 (0.26), residues: 388
  sheet:  1.16 (0.41), residues: 181
  loop : -0.94 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.012   0.001   TYR A 501 
 ARG   0.002   0.000   ARG A  40 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3659.78 seconds
wall clock time: 65 minutes 37.92 seconds (3937.92 seconds total)