Starting phenix.real_space_refine
on Tue Mar 11 15:16:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dl6_27497/03_2025/8dl6_27497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl6_27497/03_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_27497/03_2025/8dl6_27497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_2025/8dl6_27497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_2025/8dl6_27497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl6_27497/03_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-5624/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: 5.47, per 1000 atoms: 0.89
  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: 1.67
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.84
  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: 1.74

  Time building geometry restraints manager: 1.84 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:             0.350
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.080
  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:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.740
-------------------------------------------------------------------------------
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  : 0.646 
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: 1.1530
  time to fit residues: 66.0350
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  : 0.664 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.048976 restraints weight = 93234.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 6.57
r_work: 0.2665 rms_B_bonded: 6.47 restraints_weight: 2.0000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    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 = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2659
-------------------------------------------------------------------------------
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   6282  Z= 0.299
  Angle     :  0.655   8.034   8569  Z= 0.347
  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 

*********************** 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  : 0.638 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 7
  residues processed: 48
  average time/residue: 1.0737
  time to fit residues: 54.8919
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  : 0.727 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:   40.0000
   chunk 76 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3455 r_free = 0.3455 target = 0.068584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.050591 restraints weight = 50279.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 5.03
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6282  Z= 0.208
  Angle     :  0.586   8.793   8569  Z= 0.307
  Chirality :  0.042   0.150   1025
  Planarity :  0.004   0.047   1088
  Dihedral  :  5.109  59.159    932
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.02 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.18 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.48 (0.30), residues: 867
  helix:  2.89 (0.25), residues: 386
  sheet:  0.63 (0.40), residues: 183
  loop : -1.48 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.010   0.001   PHE C  91 
 TYR   0.008   0.001   TYR C 111 
 ARG   0.002   0.000   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
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7723 (mm-30)
  outliers start: 18
  outliers final: 5
  residues processed: 53
  average time/residue: 1.2713
  time to fit residues: 70.9732
Evaluate side-chains
  37 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 62 optimal weight:   50.0000
   chunk 0 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.3487 r_free = 0.3487 target = 0.070180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.052450 restraints weight = 41302.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 4.58
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6282  Z= 0.161
  Angle     :  0.572   9.307   8569  Z= 0.291
  Chirality :  0.041   0.155   1025
  Planarity :  0.004   0.044   1088
  Dihedral  :  4.597  59.533    930
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.21 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.26 %
    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:  0.79 (0.40), residues: 184
  loop : -1.36 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 127 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.006   0.001   TYR C 111 
 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
  60 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9191 (m) cc_final: 0.8835 (m)
REVERT: C   51 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9315 (m)
REVERT: D   29 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7919 (mm-30)
  outliers start: 19
  outliers final: 8
  residues processed: 57
  average time/residue: 1.0228
  time to fit residues: 62.2091
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  : 0.650 
-------------------------------------------------------------------------------
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 67 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0070
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 64 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.5804

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.069117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.050786 restraints weight = 83308.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 6.26
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2355

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= 0.190
  Angle     :  0.581   9.490   8569  Z= 0.296
  Chirality :  0.041   0.156   1025
  Planarity :  0.004   0.047   1088
  Dihedral  :  4.569  59.684    930
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.67 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.79 %
    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:  1.93 (0.30), residues: 867
  helix:  3.17 (0.25), residues: 386
  sheet:  0.93 (0.41), residues: 179
  loop : -1.14 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.008   0.001   TYR A 538 
 ARG   0.004   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
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 CYS cc_start: 0.9154 (m) cc_final: 0.8897 (m)
REVERT: D   29 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7896 (mm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 57
  average time/residue: 1.1796
  time to fit residues: 71.1300
Evaluate side-chains
  49 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
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  509 ILE
Chi-restraints excluded: chain A residue  553 CYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 55 optimal weight:   30.0000
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    0.2980
   chunk 27 optimal weight:   10.0000
   chunk 83 optimal weight:   30.0000
   chunk 70 optimal weight:    0.0570
   chunk 57 optimal weight:   30.0000
   chunk 63 optimal weight:   30.0000
   chunk 68 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.5898

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.053315 restraints weight = 61361.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 5.56
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6282  Z= 0.144
  Angle     :  0.594   9.885   8569  Z= 0.294
  Chirality :  0.041   0.164   1025
  Planarity :  0.004   0.052   1088
  Dihedral  :  4.463  58.402    930
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.63 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.54 %
    Favored  : 74.24 %
  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:  2.13 (0.30), residues: 867
  helix:  3.37 (0.25), residues: 386
  sheet:  1.08 (0.42), residues: 179
  loop : -1.13 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 127 
 HIS   0.004   0.001   HIS A 507 
 PHE   0.011   0.001   PHE A 508 
 TYR   0.007   0.001   TYR C 111 
 ARG   0.002   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
  61 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.9225 (tpp) cc_final: 0.8800 (tpp)
REVERT: D   29 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7849 (mm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 58
  average time/residue: 1.0507
  time to fit residues: 64.9488
Evaluate side-chains
  44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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 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   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:    8.9990
   chunk 85 optimal weight:   30.0000
   chunk 59 optimal weight:   50.0000
   chunk 8 optimal weight:    4.9990
   chunk 60 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
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
C  57 GLN

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 = 0.067869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.049947 restraints weight = 52715.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 5.10
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6282  Z= 0.238
  Angle     :  0.625  10.023   8569  Z= 0.319
  Chirality :  0.042   0.186   1025
  Planarity :  0.004   0.055   1088
  Dihedral  :  4.507  57.331    930
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.67 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.61 %
    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:  1.98 (0.30), residues: 867
  helix:  3.14 (0.25), residues: 385
  sheet:  1.06 (0.41), residues: 179
  loop : -1.07 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.010   0.001   PHE A 360 
 TYR   0.010   0.001   TYR A 538 
 ARG   0.003   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
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   29 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7846 (mm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 51
  average time/residue: 1.1649
  time to fit residues: 62.9762
Evaluate side-chains
  42 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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   66 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 78 optimal weight:   40.0000
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 79 optimal weight:   40.0000
   chunk 11 optimal weight:   30.0000
   chunk 66 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3367 r_free = 0.3367 target = 0.063114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.044776 restraints weight = 62142.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 5.44
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062   6282  Z= 0.526
  Angle     :  0.776  10.242   8569  Z= 0.406
  Chirality :  0.046   0.163   1025
  Planarity :  0.005   0.054   1088
  Dihedral  :  4.880  56.791    930
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.48 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.79 %
    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:  1.57 (0.30), residues: 867
  helix:  2.59 (0.25), residues: 388
  sheet:  0.94 (0.40), residues: 178
  loop : -1.05 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 224 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.009   0.002   PHE A 551 
 TYR   0.018   0.002   TYR A 501 
 ARG   0.004   0.001   ARG C  81 

*********************** 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
  51 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.649 
Fit side-chains
REVERT: D   29 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: D   59 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (tpp80)
REVERT: D   65 GLU cc_start: 0.8684 (mt-10) cc_final: 0.7996 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 49
  average time/residue: 1.3987
  time to fit residues: 72.0939
Evaluate side-chains
  44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain D residue   59 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 21 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 81 optimal weight:   40.0000
   chunk 12 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.068432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.049780 restraints weight = 95813.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 6.78
r_work: 0.2727 rms_B_bonded: 6.72 restraints_weight: 2.0000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2972

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     :  0.668  12.276   8569  Z= 0.334
  Chirality :  0.041   0.177   1025
  Planarity :  0.004   0.055   1088
  Dihedral  :  4.172  47.388    927
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.86 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 24.51 %
    Favored  : 73.52 %
  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:  3.03 (0.25), residues: 390
  sheet:  1.12 (0.40), residues: 185
  loop : -1.06 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  69 
 HIS   0.002   0.001   HIS A 125 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.007   0.001   TYR A 501 
 ARG   0.002   0.000   ARG A 178 

*********************** 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
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8135 (mm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 52
  average time/residue: 1.4169
  time to fit residues: 77.6728
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 22 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 80 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 85 optimal weight:   50.0000
   chunk 72 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.3469 r_free = 0.3469 target = 0.068003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.049792 restraints weight = 90423.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 6.61
r_work: 0.2729 rms_B_bonded: 6.60 restraints_weight: 2.0000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6282  Z= 0.199
  Angle     :  0.670  13.646   8569  Z= 0.335
  Chirality :  0.041   0.176   1025
  Planarity :  0.004   0.057   1088
  Dihedral  :  4.069  47.049    927
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.21 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 25.22 %
    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:  2.04 (0.30), residues: 867
  helix:  3.08 (0.25), residues: 387
  sheet:  1.19 (0.40), residues: 179
  loop : -0.98 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  69 
 HIS   0.002   0.000   HIS A 535 
 PHE   0.008   0.001   PHE A 360 
 TYR   0.008   0.001   TYR A 501 
 ARG   0.005   0.000   ARG D  59 

********************** 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: 10
    poor density    : 43
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8575 (mtp) cc_final: 0.7915 (mmt)
REVERT: C  127 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9196 (mmmm)
REVERT: D   29 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8061 (mm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 53
  average time/residue: 1.2795
  time to fit residues: 71.4959
Evaluate side-chains
  50 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  101 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:   50.0000
   chunk 64 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   chunk 53 optimal weight:    0.0770
   chunk 81 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9942

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.069796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.052196 restraints weight = 67148.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 5.97
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    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 = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6282  Z= 0.190
  Angle     :  0.684  14.040   8569  Z= 0.339
  Chirality :  0.041   0.165   1025
  Planarity :  0.004   0.056   1088
  Dihedral  :  4.089  46.601    927
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.32 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 25.58 %
    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:  2.05 (0.30), residues: 867
  helix:  3.08 (0.26), residues: 387
  sheet:  1.22 (0.40), residues: 179
  loop : -0.99 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  69 
 HIS   0.001   0.000   HIS A 535 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.010   0.001   TYR A 501 
 ARG   0.004   0.000   ARG D  59 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3554.99 seconds
wall clock time: 61 minutes 26.97 seconds (3686.97 seconds total)