Starting phenix.real_space_refine
on Tue Feb  3 22:52:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uyn_64619/02_2026/9uyn_64619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uyn_64619/02_2026/9uyn_64619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uyn_64619/02_2026/9uyn_64619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uyn_64619/02_2026/9uyn_64619.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uyn_64619/02_2026/9uyn_64619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uyn_64619/02_2026/9uyn_64619.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.053
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
     P       6      5.49       5
     S      26      5.16       5
     C    4865      2.51       5
     N    1247      2.21       5
     O    1359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7503
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2361
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 10, 'TRANS': 282}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 62
    Chain: "A"
      Number of atoms: 2613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2613
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 27, 'TRANS': 313}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 74
    Chain: "B"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 825
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1686
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 213}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.43, per 1000 atoms: 0.19
  Number of scatterers: 7503
  At special positions: 0
  Unit cell: (107.1, 83.538, 130.662, 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)
     S      26     16.00
     P       6     15.00
     O    1359      8.00
     N    1247      7.00
     C    4865      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 143 " - pdb=" SG  CYS A 249 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 220 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 286.2 milliseconds
  

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 13 sheets defined
      25.2% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'R' and resid 36 through 65
      removed outlier: 4.656A  pdb=" N   VAL R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
      Proline residue:  R  54  - end of helix
    Processing helix  chain 'R' and resid 73 through 99
      Proline residue:  R  91  - end of helix
      removed outlier: 3.823A  pdb=" N   MET R  99 " --> pdb=" O   SER R  95 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 106 through 140
      removed outlier: 4.072A  pdb=" N   SER R 114 " --> pdb=" O   CYS R 110 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   VAL R 125 " --> pdb=" O   MET R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 141 through 146
      removed outlier: 3.827A  pdb=" N   SER R 145 " --> pdb=" O   HIS R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 175
      Proline residue:  R 171  - end of helix
    Processing helix  chain 'R' and resid 201 through 230
      Proline residue:  R 218  - end of helix
    Processing helix  chain 'R' and resid 244 through 274
      removed outlier: 3.538A  pdb=" N   VAL R 251 " --> pdb=" O   THR R 247 " (cutoff:3.500A)
      Proline residue:  R 261  - end of helix
      removed outlier: 4.571A  pdb=" N   HIS R 274 " --> pdb=" O   LEU R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 307
      removed outlier: 4.110A  pdb=" N   ALA R 284 " --> pdb=" O   HIS R 280 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 4.265A  pdb=" N   GLY R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   PHE R 294 " --> pdb=" O   THR R 290 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER R 297 " --> pdb=" O   ALA R 293 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   CYS R 298 " --> pdb=" O   PHE R 294 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASN R 300 " --> pdb=" O   ASN R 296 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 317
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'B' and resid 61 through 64
      removed outlier: 4.101A  pdb=" N   LYS B  64 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 64'
    Processing helix  chain 'C' and resid 80 through 84
      removed outlier: 4.102A  pdb=" N   PHE C  84 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 176 through 181
    Processing sheet with id=AA2, first strand: chain 'R' and resid 1361 through 1364
      removed outlier: 3.569A  pdb=" N   LYS A  11 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A  19 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34
      removed outlier: 3.696A  pdb=" N   VAL A 171 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.717A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   VAL A  53 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   GLN A  85 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL A  55 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ASN A  83 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ALA A  59 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=AA6, first strand: chain 'A' and resid 183 through 186
      removed outlier: 3.501A  pdb=" N   SER A 202 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 207 through 209
      removed outlier: 3.617A  pdb=" N   VAL A 325 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 9.288A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS A 230 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   GLU A 257 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   ILE A 233 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.615A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B  80 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   CYS B  22 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL B  78 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59
      removed outlier: 5.607A  pdb=" N   LEU B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ARG B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN B  96 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7
      removed outlier: 3.723A  pdb=" N   THR C   6 " --> pdb=" O   ARG C  25 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG C  25 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.669A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 131
    Processing sheet with id=AB4, first strand: chain 'C' and resid 181 through 184
      removed outlier: 6.665A  pdb=" N   TRP C 160 " --> pdb=" O   VAL C 172 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   SER C 174 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ILE C 158 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   SER C 176 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
      removed outlier: 8.822A  pdb=" N   SER C 156 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG C 224 " --> pdb=" O   LEU C 231 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   LEU C 231 " --> pdb=" O   ARG C 224 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    927 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: 1.08

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2317
        1.34 -     1.46: 1830
        1.46 -     1.58: 3487
        1.58 -     1.69: 22
        1.69 -     1.81: 36
  Bond restraints: 7692
  Sorted by residual:
  bond pdb=" C10 PAM R1401 "
       pdb=" C9  PAM R1401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.529 -0.197 2.00e-02 2.50e+03 9.73e+01
  bond pdb=" OG1 TPO R1359 "
       pdb=" P   TPO R1359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" OG1 TPO R1360 "
       pdb=" P   TPO R1360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" O2P TPO R1359 "
       pdb=" P   TPO R1359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" O3P TPO R1360 "
       pdb=" P   TPO R1360 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 7687 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 10431
        2.85 -     5.69: 51
        5.69 -     8.54: 5
        8.54 -    11.38: 2
       11.38 -    14.23: 4
  Bond angle restraints: 10493
  Sorted by residual:
  angle pdb=" C11 PAM R1401 "
        pdb=" C10 PAM R1401 "
        pdb=" C9  PAM R1401 "
      ideal   model   delta    sigma   weight residual
     126.89  112.66   14.23 3.00e+00 1.11e-01 2.25e+01
  angle pdb=" C10 PAM R1401 "
        pdb=" C9  PAM R1401 "
        pdb=" C8  PAM R1401 "
      ideal   model   delta    sigma   weight residual
     126.57  112.67   13.90 3.00e+00 1.11e-01 2.15e+01
  angle pdb=" CB  TPO R1360 "
        pdb=" OG1 TPO R1360 "
        pdb=" P   TPO R1360 "
      ideal   model   delta    sigma   weight residual
     119.31  107.19   12.12 3.00e+00 1.11e-01 1.63e+01
  angle pdb=" CB  TPO R1359 "
        pdb=" OG1 TPO R1359 "
        pdb=" P   TPO R1359 "
      ideal   model   delta    sigma   weight residual
     119.31  107.79   11.52 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" N   VAL R  71 "
        pdb=" CA  VAL R  71 "
        pdb=" C   VAL R  71 "
      ideal   model   delta    sigma   weight residual
     106.21  110.29   -4.08 1.07e+00 8.73e-01 1.46e+01
  ... (remaining 10488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 4097
       16.49 -    32.98: 335
       32.98 -    49.47: 65
       49.47 -    65.95: 13
       65.95 -    82.44: 6
  Dihedral angle restraints: 4516
    sinusoidal: 1689
      harmonic: 2827
  Sorted by residual:
  dihedral pdb=" CB  CYS R 110 "
           pdb=" SG  CYS R 110 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.44   82.44     1      1.00e+01 1.00e-02 8.34e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.59   50.41     1      1.00e+01 1.00e-02 3.48e+01
  dihedral pdb=" CA  MET R  99 "
           pdb=" C   MET R  99 "
           pdb=" N   ASN R 100 "
           pdb=" CA  ASN R 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.16  -27.84     0      5.00e+00 4.00e-02 3.10e+01
  ... (remaining 4513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 754
       0.027 -    0.055: 285
       0.055 -    0.082: 88
       0.082 -    0.109: 67
       0.109 -    0.137: 24
  Chirality restraints: 1218
  Sorted by residual:
  chirality pdb=" CA  THR R 260 "
            pdb=" N   THR R 260 "
            pdb=" C   THR R 260 "
            pdb=" CB  THR R 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  ILE A 233 "
            pdb=" N   ILE A 233 "
            pdb=" C   ILE A 233 "
            pdb=" CB  ILE A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  ILE C  22 "
            pdb=" N   ILE C  22 "
            pdb=" C   ILE C  22 "
            pdb=" CB  ILE C  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 1215 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 170 "    0.041 5.00e-02 4.00e+02   6.25e-02 6.25e+00
        pdb=" N   PRO R 171 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 171 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 171 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 PAM R1401 "    0.024 2.00e-02 2.50e+03   2.44e-02 5.96e+00
        pdb=" C11 PAM R1401 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8  PAM R1401 "   -0.024 2.00e-02 2.50e+03
        pdb=" C9  PAM R1401 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 213 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.26e+00
        pdb=" C   ILE R 213 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ILE R 213 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY R 214 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 239
        2.72 -     3.26: 7095
        3.26 -     3.81: 11777
        3.81 -     4.35: 14456
        4.35 -     4.90: 25639
  Nonbonded interactions: 59206
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 204 "
            pdb=" OH  TYR A 208 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   TYR C  50 "
            pdb=" OH  TYR C  92 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OD1 ASP A  26 "
            pdb=" NE2 HIS A 362 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" NH2 ARG A  25 "
            pdb=" O   VAL A 167 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" NH1 ARG A  62 "
            pdb=" O   GLY A  64 "
     model   vdw
     2.290 3.120
  ... (remaining 59201 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=1.00 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:             1.030
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.670
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:5.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
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      :  0.004   0.197   7697  Z= 0.201
  Angle     :  0.592  14.229  10503  Z= 0.292
  Chirality :  0.040   0.137   1218
  Planarity :  0.004   0.063   1296
  Dihedral  : 12.748  82.179   2677
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.29), residues: 941
  helix:  1.51 (0.36), residues: 222
  sheet:  0.99 (0.32), residues: 279
  loop : -1.17 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  62 
 TYR   0.007   0.001   TYR C 228 
 PHE   0.013   0.001   PHE B  29 
 TRP   0.009   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7692)
  covalent geometry    : angle       0.59215 (10493)
  SS BOND              : bond        0.00124 (    5)
  SS BOND              : angle       0.56524 (   10)
  hydrogen bonds       : bond        0.19170 (  331)
  hydrogen bonds       : angle       7.60029 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.181 
Fit side-chains
REVERT: R  121 MET cc_start: 0.7920 (ttm) cc_final: 0.7606 (ttp)
REVERT: A   32 ASP cc_start: 0.7898 (p0) cc_final: 0.7650 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.4544
  time to fit residues: 52.1124
Evaluate side-chains
  80 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
C  28 GLN
C  39 GLN
C 236 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.188498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.150081 restraints weight = 7993.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.30
r_work: 0.3413 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7697  Z= 0.182
  Angle     :  0.611   6.745  10503  Z= 0.319
  Chirality :  0.045   0.160   1218
  Planarity :  0.005   0.062   1296
  Dihedral  :  6.663  68.794   1069
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.13 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.29), residues: 941
  helix:  1.54 (0.36), residues: 217
  sheet:  0.78 (0.31), residues: 300
  loop : -1.09 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A   7 
 TYR   0.016   0.002   TYR C  50 
 PHE   0.019   0.002   PHE A 268 
 TRP   0.013   0.001   TRP C 227 
 HIS   0.007   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7692)
  covalent geometry    : angle       0.60943 (10493)
  SS BOND              : bond        0.00997 (    5)
  SS BOND              : angle       1.39686 (   10)
  hydrogen bonds       : bond        0.04212 (  331)
  hydrogen bonds       : angle       5.39457 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.227 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.8008 (tp) cc_final: 0.7777 (tp)
REVERT: C    5 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.5865 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 99
  average time/residue: 0.4739
  time to fit residues: 49.8869
Evaluate side-chains
  92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain A residue  118 GLU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain C residue    5 MET
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 79 optimal weight:    0.0050
   chunk 60 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A 172 GLN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.188109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.148469 restraints weight = 7821.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.29
r_work: 0.3337 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7697  Z= 0.125
  Angle     :  0.549   7.649  10503  Z= 0.283
  Chirality :  0.042   0.150   1218
  Planarity :  0.004   0.061   1296
  Dihedral  :  6.433  67.682   1069
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 11.90 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.28), residues: 941
  helix:  1.56 (0.36), residues: 218
  sheet:  0.80 (0.31), residues: 285
  loop : -1.15 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 176 
 TYR   0.016   0.001   TYR C 228 
 PHE   0.019   0.001   PHE A 268 
 TRP   0.011   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7692)
  covalent geometry    : angle       0.54842 (10493)
  SS BOND              : bond        0.00224 (    5)
  SS BOND              : angle       0.96933 (   10)
  hydrogen bonds       : bond        0.03779 (  331)
  hydrogen bonds       : angle       4.96930 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.191 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.7929 (tp) cc_final: 0.7671 (tp)
REVERT: C   78 SER cc_start: 0.8105 (m) cc_final: 0.7641 (p)
  outliers start: 22
  outliers final: 10
  residues processed: 96
  average time/residue: 0.3939
  time to fit residues: 40.4683
Evaluate side-chains
  89 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain C residue   61 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    0.0970
   chunk 69 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
C 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.185980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.147519 restraints weight = 7967.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.41
r_work: 0.3282 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7697  Z= 0.133
  Angle     :  0.557   8.024  10503  Z= 0.286
  Chirality :  0.042   0.153   1218
  Planarity :  0.004   0.061   1296
  Dihedral  :  6.412  68.102   1069
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 11.77 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.28), residues: 941
  helix:  1.46 (0.36), residues: 223
  sheet:  0.62 (0.30), residues: 294
  loop : -1.17 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.017   0.001   TYR C 228 
 PHE   0.022   0.002   PHE A 268 
 TRP   0.010   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7692)
  covalent geometry    : angle       0.55599 (10493)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.99590 (   10)
  hydrogen bonds       : bond        0.03570 (  331)
  hydrogen bonds       : angle       4.77923 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.199 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7733 (tp)
REVERT: C   78 SER cc_start: 0.8252 (m) cc_final: 0.7907 (p)
  outliers start: 31
  outliers final: 18
  residues processed: 102
  average time/residue: 0.4160
  time to fit residues: 45.5668
Evaluate side-chains
  99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  212 ILE
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   61 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 93 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0770
   chunk 40 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
R 296 ASN
A 162 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.188339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.147415 restraints weight = 7958.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.62
r_work: 0.3409 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7697  Z= 0.101
  Angle     :  0.521   7.480  10503  Z= 0.268
  Chirality :  0.041   0.146   1218
  Planarity :  0.004   0.061   1296
  Dihedral  :  6.413  70.966   1069
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.42 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.28), residues: 941
  helix:  1.49 (0.36), residues: 224
  sheet:  0.64 (0.30), residues: 295
  loop : -1.19 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 176 
 TYR   0.014   0.001   TYR C 228 
 PHE   0.022   0.001   PHE A 268 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7692)
  covalent geometry    : angle       0.52086 (10493)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.71377 (   10)
  hydrogen bonds       : bond        0.03232 (  331)
  hydrogen bonds       : angle       4.61929 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.281 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.8047 (tp) cc_final: 0.7744 (tp)
REVERT: R  282 MET cc_start: 0.5360 (ttm) cc_final: 0.4482 (tmm)
REVERT: A   46 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7354 (mp0)
REVERT: A  221 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7794 (t)
REVERT: A  283 GLU cc_start: 0.8204 (pm20) cc_final: 0.7965 (pm20)
  outliers start: 22
  outliers final: 17
  residues processed: 101
  average time/residue: 0.3845
  time to fit residues: 41.9305
Evaluate side-chains
  99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  167 LYS
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0070
   chunk 16 optimal weight:    9.9990
   chunk 59 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A  30 HIS
A 162 ASN
A 248 GLN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.186190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.145306 restraints weight = 7938.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.70
r_work: 0.3372 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7697  Z= 0.123
  Angle     :  0.538   7.400  10503  Z= 0.277
  Chirality :  0.042   0.152   1218
  Planarity :  0.004   0.061   1296
  Dihedral  :  6.392  70.679   1069
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 13.42 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.28), residues: 941
  helix:  1.51 (0.36), residues: 224
  sheet:  0.59 (0.31), residues: 294
  loop : -1.15 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 176 
 TYR   0.016   0.001   TYR C 228 
 PHE   0.023   0.001   PHE A 268 
 TRP   0.010   0.001   TRP R  75 
 HIS   0.002   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7692)
  covalent geometry    : angle       0.53755 (10493)
  SS BOND              : bond        0.00214 (    5)
  SS BOND              : angle       0.79088 (   10)
  hydrogen bonds       : bond        0.03394 (  331)
  hydrogen bonds       : angle       4.59821 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 0.198 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7789 (tp)
REVERT: R  282 MET cc_start: 0.5300 (ttm) cc_final: 0.4178 (tmm)
REVERT: A   46 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7453 (mp0)
REVERT: A  221 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7828 (t)
REVERT: C   78 SER cc_start: 0.8255 (m) cc_final: 0.7956 (p)
  outliers start: 31
  outliers final: 20
  residues processed: 100
  average time/residue: 0.3833
  time to fit residues: 41.0638
Evaluate side-chains
  101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  167 LYS
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0050
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A 162 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.183330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.142268 restraints weight = 7856.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.37
r_work: 0.3289 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7697  Z= 0.138
  Angle     :  0.558   7.288  10503  Z= 0.288
  Chirality :  0.042   0.164   1218
  Planarity :  0.004   0.062   1296
  Dihedral  :  6.492  69.449   1069
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 13.80 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.28), residues: 941
  helix:  1.52 (0.36), residues: 223
  sheet:  0.60 (0.31), residues: 283
  loop : -1.16 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.018   0.001   TYR C 228 
 PHE   0.021   0.002   PHE A 268 
 TRP   0.011   0.001   TRP R  75 
 HIS   0.002   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7692)
  covalent geometry    : angle       0.55747 (10493)
  SS BOND              : bond        0.00217 (    5)
  SS BOND              : angle       0.87673 (   10)
  hydrogen bonds       : bond        0.03552 (  331)
  hydrogen bonds       : angle       4.65368 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.186 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7658 (tp)
REVERT: R  282 MET cc_start: 0.4959 (ttm) cc_final: 0.3970 (tmm)
REVERT: A   46 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7223 (mp0)
REVERT: A  221 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7636 (t)
REVERT: A  297 ASP cc_start: 0.8300 (p0) cc_final: 0.7968 (p0)
REVERT: B   34 MET cc_start: 0.6980 (mmm) cc_final: 0.6767 (mmt)
REVERT: C   78 SER cc_start: 0.8076 (m) cc_final: 0.7567 (p)
REVERT: C  145 SER cc_start: 0.7851 (m) cc_final: 0.7635 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 97
  average time/residue: 0.3597
  time to fit residues: 37.4930
Evaluate side-chains
  97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  167 LYS
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0070
   chunk 74 optimal weight:    0.0570
   chunk 71 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A 162 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.184904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.143713 restraints weight = 7916.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.38
r_work: 0.3309 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7697  Z= 0.113
  Angle     :  0.529   7.884  10503  Z= 0.273
  Chirality :  0.041   0.161   1218
  Planarity :  0.004   0.062   1296
  Dihedral  :  6.456  71.147   1069
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.18 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.28), residues: 941
  helix:  1.45 (0.35), residues: 228
  sheet:  0.59 (0.31), residues: 283
  loop : -1.19 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 176 
 TYR   0.016   0.001   TYR C 228 
 PHE   0.026   0.001   PHE A 268 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7692)
  covalent geometry    : angle       0.52859 (10493)
  SS BOND              : bond        0.00205 (    5)
  SS BOND              : angle       0.72638 (   10)
  hydrogen bonds       : bond        0.03298 (  331)
  hydrogen bonds       : angle       4.58580 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.251 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.7925 (tp) cc_final: 0.7613 (tp)
REVERT: R  282 MET cc_start: 0.4953 (ttm) cc_final: 0.3960 (tmm)
REVERT: A   46 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7252 (mp0)
REVERT: A  221 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7638 (t)
REVERT: A  283 GLU cc_start: 0.8218 (pm20) cc_final: 0.7982 (pm20)
REVERT: A  297 ASP cc_start: 0.8255 (p0) cc_final: 0.7930 (p0)
REVERT: B   34 MET cc_start: 0.6924 (mmm) cc_final: 0.6719 (mmt)
REVERT: C   78 SER cc_start: 0.8065 (m) cc_final: 0.7724 (p)
  outliers start: 27
  outliers final: 21
  residues processed: 97
  average time/residue: 0.3591
  time to fit residues: 37.3060
Evaluate side-chains
  96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  167 LYS
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  239 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0370
   chunk 84 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A 162 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.182891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.141895 restraints weight = 7834.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.48
r_work: 0.3293 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7697  Z= 0.147
  Angle     :  0.573   8.030  10503  Z= 0.294
  Chirality :  0.043   0.167   1218
  Planarity :  0.004   0.063   1296
  Dihedral  :  6.511  69.908   1069
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.81 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.28), residues: 941
  helix:  1.41 (0.35), residues: 228
  sheet:  0.56 (0.32), residues: 283
  loop : -1.20 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 176 
 TYR   0.018   0.001   TYR C 228 
 PHE   0.026   0.002   PHE A 268 
 TRP   0.011   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7692)
  covalent geometry    : angle       0.57293 (10493)
  SS BOND              : bond        0.00247 (    5)
  SS BOND              : angle       0.86518 (   10)
  hydrogen bonds       : bond        0.03578 (  331)
  hydrogen bonds       : angle       4.64320 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.272 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7639 (tp)
REVERT: R  282 MET cc_start: 0.4899 (ttm) cc_final: 0.3861 (tmm)
REVERT: A   46 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7256 (mp0)
REVERT: A  221 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7636 (t)
REVERT: A  297 ASP cc_start: 0.8332 (p0) cc_final: 0.7857 (p0)
REVERT: C   78 SER cc_start: 0.8066 (m) cc_final: 0.7558 (p)
  outliers start: 26
  outliers final: 19
  residues processed: 93
  average time/residue: 0.3626
  time to fit residues: 36.3449
Evaluate side-chains
  94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 92 optimal weight:    0.1980
   chunk 79 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A 162 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.183838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.142443 restraints weight = 7842.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.26
r_work: 0.3321 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7697  Z= 0.127
  Angle     :  0.552   8.002  10503  Z= 0.285
  Chirality :  0.042   0.163   1218
  Planarity :  0.004   0.063   1296
  Dihedral  :  6.530  70.878   1069
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.70 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.28), residues: 941
  helix:  1.42 (0.35), residues: 228
  sheet:  0.57 (0.32), residues: 283
  loop : -1.20 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 176 
 TYR   0.017   0.001   TYR C 228 
 PHE   0.027   0.002   PHE A 268 
 TRP   0.013   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7692)
  covalent geometry    : angle       0.55201 (10493)
  SS BOND              : bond        0.00211 (    5)
  SS BOND              : angle       0.75694 (   10)
  hydrogen bonds       : bond        0.03443 (  331)
  hydrogen bonds       : angle       4.62580 (  927)

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

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

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1882 Ramachandran restraints generated.
    941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.181 
Fit side-chains
REVERT: R   88 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7615 (tp)
REVERT: R  282 MET cc_start: 0.4896 (ttm) cc_final: 0.3868 (tmm)
REVERT: A   46 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7296 (mp0)
REVERT: A  221 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7660 (t)
REVERT: A  297 ASP cc_start: 0.8277 (p0) cc_final: 0.7842 (p0)
REVERT: C   78 SER cc_start: 0.8072 (m) cc_final: 0.7574 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 89
  average time/residue: 0.3801
  time to fit residues: 36.3998
Evaluate side-chains
  93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  193 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0040
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
A 162 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.183929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.142404 restraints weight = 7810.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.12
r_work: 0.3335 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7697  Z= 0.134
  Angle     :  0.575  11.402  10503  Z= 0.294
  Chirality :  0.043   0.164   1218
  Planarity :  0.004   0.063   1296
  Dihedral  :  6.542  70.865   1069
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.70 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.28), residues: 941
  helix:  1.40 (0.35), residues: 228
  sheet:  0.62 (0.32), residues: 281
  loop : -1.22 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 176 
 TYR   0.017   0.001   TYR C 228 
 PHE   0.027   0.002   PHE A 268 
 TRP   0.012   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7692)
  covalent geometry    : angle       0.57377 (10493)
  SS BOND              : bond        0.00284 (    5)
  SS BOND              : angle       1.38539 (   10)
  hydrogen bonds       : bond        0.03501 (  331)
  hydrogen bonds       : angle       4.62901 (  927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2462.43 seconds
wall clock time: 42 minutes 35.14 seconds (2555.14 seconds total)