Starting phenix.real_space_refine
on Wed Feb 12 01:32:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ugy_42241/02_2025/8ugy_42241.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ugy_42241/02_2025/8ugy_42241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ugy_42241/02_2025/8ugy_42241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ugy_42241/02_2025/8ugy_42241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ugy_42241/02_2025/8ugy_42241.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ugy_42241/02_2025/8ugy_42241.cif"
  }
  resolution = 3.31
  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=  -0.002 sd=   0.107
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4503      2.51       5
     N    1159      2.21       5
     O    1256      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6970
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1750
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2558
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "G"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 391
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
    Chain: "R"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2110
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 8, 'TRANS': 255}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "R"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 161
          Unusual residues: {'CLR': 5, 'WRU': 1}
          Classifications: {'undetermined': 6, 'water': 1}
          Link IDs: {None: 6}
  Time building chain proxies: 5.05, per 1000 atoms: 0.72
  Number of scatterers: 6970
  At special positions: 0
  Unit cell: (76.968, 99.417, 124.004, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1256      8.00
     N    1159      7.00
     C    4503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 173 " 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: 1.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      48.4% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.064A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.604A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.286A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.035A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.817A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.618A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 328 through 351
      removed outlier: 3.585A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 4.225A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'R' and resid 21 through 50
      removed outlier: 3.571A  pdb=" N   THR R  37 " --> pdb=" O   THR R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 75
    Processing helix  chain 'R' and resid 75 through 85
    Processing helix  chain 'R' and resid 93 through 126
      removed outlier: 3.890A  pdb=" N   ILE R 110 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 134
      removed outlier: 4.308A  pdb=" N   ARG R 132 " --> pdb=" O   ILE R 128 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS R 133 " --> pdb=" O   GLU R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 135 through 153
    Processing helix  chain 'R' and resid 155 through 160
      removed outlier: 3.843A  pdb=" N   PHE R 159 " --> pdb=" O   MET R 155 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TRP R 160 " --> pdb=" O   PRO R 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 155 through 160'
    Processing helix  chain 'R' and resid 179 through 191
    Processing helix  chain 'R' and resid 191 through 215
      removed outlier: 3.550A  pdb=" N   LYS R 215 " --> pdb=" O   SER R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 316
      removed outlier: 3.625A  pdb=" N   PHE R 300 " --> pdb=" O   ILE R 296 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 322 through 335
    Processing helix  chain 'R' and resid 335 through 346
      Proline residue:  R 341  - end of helix
    Processing helix  chain 'R' and resid 348 through 358
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.322A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.243A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.564A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.530A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.581A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.637A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1134 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: 1.89

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2185
        1.35 -     1.47: 1700
        1.47 -     1.59: 3161
        1.59 -     1.71: 0
        1.71 -     1.83: 74
  Bond restraints: 7120
  Sorted by residual:
  bond pdb=" C3  CLR R 404 "
       pdb=" O1  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.17e+00
  bond pdb=" C3  CLR R 403 "
       pdb=" O1  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.16e+00
  bond pdb=" C3  CLR R 405 "
       pdb=" O1  CLR R 405 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C3  CLR R 402 "
       pdb=" O1  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.12e+00
  bond pdb=" C3  CLR R 401 "
       pdb=" O1  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.07e+00
  ... (remaining 7115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 9373
        1.34 -     2.69: 230
        2.69 -     4.03: 42
        4.03 -     5.37: 20
        5.37 -     6.71: 7
  Bond angle restraints: 9672
  Sorted by residual:
  angle pdb=" N   GLU A 308 "
        pdb=" CA  GLU A 308 "
        pdb=" CB  GLU A 308 "
      ideal   model   delta    sigma   weight residual
     110.39  114.73   -4.34 1.66e+00 3.63e-01 6.83e+00
  angle pdb=" C   PHE A 307 "
        pdb=" N   GLU A 308 "
        pdb=" CA  GLU A 308 "
      ideal   model   delta    sigma   weight residual
     120.72  116.59    4.13 1.67e+00 3.59e-01 6.12e+00
  angle pdb=" C   VAL R 115 "
        pdb=" CA  VAL R 115 "
        pdb=" CB  VAL R 115 "
      ideal   model   delta    sigma   weight residual
     112.16  108.22    3.94 1.63e+00 3.76e-01 5.83e+00
  angle pdb=" N   MET R 155 "
        pdb=" CA  MET R 155 "
        pdb=" C   MET R 155 "
      ideal   model   delta    sigma   weight residual
     109.81  114.96   -5.15 2.21e+00 2.05e-01 5.44e+00
  angle pdb=" N   PRO R 156 "
        pdb=" CA  PRO R 156 "
        pdb=" C   PRO R 156 "
      ideal   model   delta    sigma   weight residual
     110.70  113.54   -2.84 1.22e+00 6.72e-01 5.40e+00
  ... (remaining 9667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.48: 4236
       24.48 -    48.96: 223
       48.96 -    73.43: 22
       73.43 -    97.91: 2
       97.91 -   122.39: 7
  Dihedral angle restraints: 4490
    sinusoidal: 1963
      harmonic: 2527
  Sorted by residual:
  dihedral pdb=" CB  CYS R  95 "
           pdb=" SG  CYS R  95 "
           pdb=" SG  CYS R 173 "
           pdb=" CB  CYS R 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.63  -86.63     1      1.00e+01 1.00e-02 9.04e+01
  dihedral pdb=" C1  CLR R 405 "
           pdb=" C2  CLR R 405 "
           pdb=" C3  CLR R 405 "
           pdb=" O1  CLR R 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.04   57.65  122.39     1      3.00e+01 1.11e-03 1.64e+01
  dihedral pdb=" N1  WRU R 406 "
           pdb=" C11 WRU R 406 "
           pdb=" C12 WRU R 406 "
           pdb=" N2  WRU R 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.38   62.28 -120.66     1      3.00e+01 1.11e-03 1.61e+01
  ... (remaining 4487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 748
       0.037 -    0.074: 284
       0.074 -    0.111: 79
       0.111 -    0.148: 19
       0.148 -    0.185: 2
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" C9  CLR R 402 "
            pdb=" C10 CLR R 402 "
            pdb=" C11 CLR R 402 "
            pdb=" C8  CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.26   -0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET R 155 "   -0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO R 156 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO R 156 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 156 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 WRU R 406 "   -0.005 2.00e-02 2.50e+03   1.20e-02 2.90e+00
        pdb=" C14 WRU R 406 "    0.009 2.00e-02 2.50e+03
        pdb=" C15 WRU R 406 "    0.011 2.00e-02 2.50e+03
        pdb=" C16 WRU R 406 "   -0.001 2.00e-02 2.50e+03
        pdb=" C17 WRU R 406 "   -0.014 2.00e-02 2.50e+03
        pdb=" C18 WRU R 406 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2  WRU R 406 "    0.022 2.00e-02 2.50e+03
        pdb=" N2  WRU R 406 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO G  55 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 132
        2.69 -     3.24: 6786
        3.24 -     3.80: 10978
        3.80 -     4.35: 14659
        4.35 -     4.90: 24924
  Nonbonded interactions: 57479
  Sorted by model distance:
  nonbonded pdb=" O   PRO R 341 "
            pdb=" OG1 THR R 345 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OD1 ASP A 341 "
            pdb=" NZ  LYS A 345 "
     model   vdw
     2.288 3.120
  ... (remaining 57474 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:             1.130
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.750
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
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      :  0.003   0.032   7120  Z= 0.208
  Angle     :  0.560   6.713   9672  Z= 0.290
  Chirality :  0.043   0.185   1132
  Planarity :  0.003   0.056   1170
  Dihedral  : 14.646 122.390   2842
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.71 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.36 (0.29), residues: 848
  helix:  1.66 (0.28), residues: 372
  sheet: -0.64 (0.39), residues: 167
  loop : -0.96 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.001   0.000   HIS R 177 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 203 
 ARG   0.007   0.000   ARG B 197 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8030 (ttmt)
REVERT: R  338 LEU cc_start: 0.8846 (tp) cc_final: 0.8571 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2543
  time to fit residues: 40.9083
Evaluate side-chains
  109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0020
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0270
   chunk 49 optimal weight:    0.0870
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.3424

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 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 = 0.3574 r_free = 0.3574 target = 0.147614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.110390 restraints weight = 7733.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.99
r_work: 0.3043 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7120  Z= 0.163
  Angle     :  0.536   6.496   9672  Z= 0.277
  Chirality :  0.041   0.154   1132
  Planarity :  0.004   0.055   1170
  Dihedral  :  5.410  56.889   1274
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.07 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.24 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.70 (0.30), residues: 848
  helix:  2.09 (0.27), residues: 376
  sheet: -0.65 (0.38), residues: 183
  loop : -0.93 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 207 
 PHE   0.011   0.001   PHE R 300 
 TYR   0.012   0.001   TYR R 182 
 ARG   0.007   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  255 ASN cc_start: 0.8623 (m110) cc_final: 0.8405 (m-40)
REVERT: A  349 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8081 (ttmt)
REVERT: R  124 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8227 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 117
  average time/residue: 0.2256
  time to fit residues: 34.3276
Evaluate side-chains
  116 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 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 = 0.3543 r_free = 0.3543 target = 0.145469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.107367 restraints weight = 7805.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.09
r_work: 0.2951 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7120  Z= 0.190
  Angle     :  0.499   6.051   9672  Z= 0.265
  Chirality :  0.041   0.152   1132
  Planarity :  0.003   0.055   1170
  Dihedral  :  4.945  58.038   1274
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.59 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.08 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.74 (0.30), residues: 848
  helix:  2.12 (0.27), residues: 379
  sheet: -0.69 (0.38), residues: 185
  loop : -0.88 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 182 
 ARG   0.004   0.000   ARG B 219 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A  255 ASN cc_start: 0.8550 (m110) cc_final: 0.8284 (m-40)
REVERT: A  349 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8039 (ttmt)
REVERT: A  350 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8354 (t0)
REVERT: A  353 LEU cc_start: 0.8190 (mt) cc_final: 0.7909 (mt)
REVERT: R  124 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8235 (mt)
REVERT: R  338 LEU cc_start: 0.8766 (tp) cc_final: 0.8524 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 112
  average time/residue: 0.2163
  time to fit residues: 31.5508
Evaluate side-chains
  113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.143760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.105716 restraints weight = 7871.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.09
r_work: 0.2930 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7120  Z= 0.222
  Angle     :  0.506   6.037   9672  Z= 0.268
  Chirality :  0.041   0.151   1132
  Planarity :  0.003   0.054   1170
  Dihedral  :  5.068  56.820   1274
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.18 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 12.16 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.75 (0.30), residues: 848
  helix:  2.11 (0.27), residues: 380
  sheet: -0.71 (0.39), residues: 185
  loop : -0.84 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 182 
 ARG   0.005   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A  255 ASN cc_start: 0.8609 (m110) cc_final: 0.8337 (m-40)
REVERT: A  275 GLU cc_start: 0.8727 (tt0) cc_final: 0.8464 (tt0)
REVERT: A  349 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8086 (ttmt)
REVERT: A  353 LEU cc_start: 0.8269 (mt) cc_final: 0.7993 (mt)
REVERT: G   19 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7761 (tt)
REVERT: R  124 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8069 (mp)
REVERT: R  338 LEU cc_start: 0.8764 (tp) cc_final: 0.8456 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 122
  average time/residue: 0.2063
  time to fit residues: 33.2687
Evaluate side-chains
  119 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0470
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 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 = 0.3537 r_free = 0.3537 target = 0.144911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.107267 restraints weight = 7726.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.07
r_work: 0.3012 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7120  Z= 0.174
  Angle     :  0.485   5.952   9672  Z= 0.258
  Chirality :  0.041   0.142   1132
  Planarity :  0.003   0.054   1170
  Dihedral  :  5.014  56.163   1274
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.07 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.11 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.84 (0.30), residues: 848
  helix:  2.20 (0.27), residues: 381
  sheet: -0.72 (0.39), residues: 186
  loop : -0.79 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 207 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 182 
 ARG   0.005   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8748 (tt0) cc_final: 0.8495 (tt0)
REVERT: A  349 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8182 (ttmt)
REVERT: A  353 LEU cc_start: 0.8331 (mt) cc_final: 0.8061 (mt)
REVERT: G   19 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7884 (tt)
REVERT: R  124 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: R  212 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6352 (mp)
REVERT: R  338 LEU cc_start: 0.8838 (tp) cc_final: 0.8491 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 122
  average time/residue: 0.2050
  time to fit residues: 32.5819
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.143636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.105620 restraints weight = 7823.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.09
r_work: 0.3006 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7120  Z= 0.220
  Angle     :  0.507   5.987   9672  Z= 0.268
  Chirality :  0.041   0.145   1132
  Planarity :  0.003   0.053   1170
  Dihedral  :  5.080  55.439   1274
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.30 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.78 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.71 (0.30), residues: 848
  helix:  2.05 (0.27), residues: 387
  sheet: -0.77 (0.39), residues: 181
  loop : -0.85 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R 182 
 ARG   0.005   0.000   ARG B 197 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8770 (tt0) cc_final: 0.8358 (tt0)
REVERT: A  349 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8238 (ttmt)
REVERT: B   20 ASP cc_start: 0.8046 (m-30) cc_final: 0.7707 (m-30)
REVERT: G   19 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7809 (tt)
REVERT: R  124 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8150 (mp)
REVERT: R  212 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6448 (mp)
  outliers start: 24
  outliers final: 15
  residues processed: 122
  average time/residue: 0.2072
  time to fit residues: 33.3344
Evaluate side-chains
  129 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  312 LEU
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0980
   chunk 43 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.145177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.106554 restraints weight = 7752.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.10
r_work: 0.2937 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7120  Z= 0.199
  Angle     :  0.498   5.920   9672  Z= 0.263
  Chirality :  0.041   0.142   1132
  Planarity :  0.003   0.052   1170
  Dihedral  :  5.087  54.681   1274
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.95 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.59 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.75 (0.30), residues: 848
  helix:  2.09 (0.27), residues: 388
  sheet: -0.79 (0.38), residues: 186
  loop : -0.83 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R 182 
 ARG   0.006   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7696 (t0)
REVERT: A  275 GLU cc_start: 0.8780 (tt0) cc_final: 0.8352 (tt0)
REVERT: A  308 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8290 (mp0)
REVERT: A  349 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8150 (ttmt)
REVERT: A  350 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8338 (t0)
REVERT: B   20 ASP cc_start: 0.8085 (m-30) cc_final: 0.7726 (m-30)
REVERT: B  234 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8984 (m-80)
REVERT: G   19 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7771 (tt)
REVERT: R  124 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: R  126 ASN cc_start: 0.8457 (t0) cc_final: 0.8201 (t0)
REVERT: R  212 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6374 (mp)
REVERT: R  338 LEU cc_start: 0.8785 (tp) cc_final: 0.8437 (tp)
  outliers start: 24
  outliers final: 13
  residues processed: 124
  average time/residue: 0.2022
  time to fit residues: 33.1380
Evaluate side-chains
  131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  312 LEU
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   chunk 2 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.146237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.107754 restraints weight = 7693.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.12
r_work: 0.2937 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7120  Z= 0.239
  Angle     :  0.520   5.968   9672  Z= 0.275
  Chirality :  0.042   0.144   1132
  Planarity :  0.003   0.052   1170
  Dihedral  :  5.175  53.556   1274
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.30 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.86 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.70 (0.30), residues: 848
  helix:  2.04 (0.27), residues: 388
  sheet: -0.83 (0.39), residues: 183
  loop : -0.83 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R 182 
 ARG   0.006   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7764 (t0)
REVERT: A  308 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8254 (mp0)
REVERT: A  349 LYS cc_start: 0.8632 (ttpt) cc_final: 0.8152 (ttmt)
REVERT: A  350 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8344 (t0)
REVERT: B   20 ASP cc_start: 0.8114 (m-30) cc_final: 0.7745 (m-30)
REVERT: B  234 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8948 (m-80)
REVERT: G   19 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7745 (tt)
REVERT: R  124 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8103 (mp)
REVERT: R  212 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6412 (mp)
REVERT: R  338 LEU cc_start: 0.8775 (tp) cc_final: 0.8384 (tp)
  outliers start: 24
  outliers final: 13
  residues processed: 121
  average time/residue: 0.2076
  time to fit residues: 33.1234
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  312 LEU
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.142716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.103887 restraints weight = 7870.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.12
r_work: 0.2910 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7120  Z= 0.269
  Angle     :  0.542   5.990   9672  Z= 0.285
  Chirality :  0.042   0.145   1132
  Planarity :  0.003   0.052   1170
  Dihedral  :  5.282  52.106   1274
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.07 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.41 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.70 (0.30), residues: 848
  helix:  2.06 (0.27), residues: 386
  sheet: -0.80 (0.39), residues: 177
  loop : -0.89 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R 182 
 ARG   0.006   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7819 (t0)
REVERT: A  275 GLU cc_start: 0.8802 (tt0) cc_final: 0.8357 (tt0)
REVERT: A  308 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8242 (mp0)
REVERT: A  349 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8191 (ttmt)
REVERT: A  350 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8321 (t0)
REVERT: B   20 ASP cc_start: 0.8127 (m-30) cc_final: 0.7757 (m-30)
REVERT: B  234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.9032 (m-80)
REVERT: G   19 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7743 (tt)
REVERT: R  124 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8112 (mp)
REVERT: R  212 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6337 (tt)
REVERT: R  338 LEU cc_start: 0.8777 (tp) cc_final: 0.8364 (tp)
  outliers start: 24
  outliers final: 13
  residues processed: 125
  average time/residue: 0.2084
  time to fit residues: 34.7450
Evaluate side-chains
  131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue   94 LEU
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  312 LEU
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.142307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.103425 restraints weight = 7848.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.10
r_work: 0.2912 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7120  Z= 0.266
  Angle     :  0.550   7.930   9672  Z= 0.288
  Chirality :  0.042   0.145   1132
  Planarity :  0.003   0.052   1170
  Dihedral  :  5.359  50.021   1274
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.30 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.49 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.68 (0.30), residues: 848
  helix:  2.04 (0.27), residues: 386
  sheet: -0.82 (0.40), residues: 177
  loop : -0.87 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 182 
 ARG   0.006   0.000   ARG B  19 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7790 (t0)
REVERT: A  275 GLU cc_start: 0.8826 (tt0) cc_final: 0.8367 (tt0)
REVERT: A  308 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8235 (mp0)
REVERT: A  349 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8198 (ttmt)
REVERT: A  350 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8331 (t0)
REVERT: B   10 GLU cc_start: 0.7205 (tp30) cc_final: 0.6992 (tp30)
REVERT: B  234 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.9038 (m-80)
REVERT: G   19 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7784 (tt)
REVERT: R  124 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8134 (mp)
REVERT: R  212 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6353 (tt)
REVERT: R  338 LEU cc_start: 0.8801 (tp) cc_final: 0.8373 (tp)
  outliers start: 21
  outliers final: 14
  residues processed: 122
  average time/residue: 0.2162
  time to fit residues: 34.8502
Evaluate side-chains
  131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   45 MET
Chi-restraints excluded: chain R residue   94 LEU
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  155 MET
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  312 LEU
Chi-restraints excluded: chain R residue  321 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 64 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.143647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.105669 restraints weight = 7714.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.03
r_work: 0.2955 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7120  Z= 0.202
  Angle     :  0.522   6.822   9672  Z= 0.274
  Chirality :  0.041   0.141   1132
  Planarity :  0.003   0.052   1170
  Dihedral  :  5.251  48.979   1274
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.07 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.35 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.78 (0.30), residues: 848
  helix:  2.09 (0.27), residues: 388
  sheet: -0.78 (0.40), residues: 178
  loop : -0.77 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 182 
 ARG   0.006   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3978.23 seconds
wall clock time: 71 minutes 27.85 seconds (4287.85 seconds total)