Starting phenix.real_space_refine
on Thu Mar 13 21:06:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p02_13141/03_2025/7p02_13141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p02_13141/03_2025/7p02_13141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p02_13141/03_2025/7p02_13141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p02_13141/03_2025/7p02_13141.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p02_13141/03_2025/7p02_13141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p02_13141/03_2025/7p02_13141.cif"
  }
  resolution = 2.87
  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=  -0.001 sd=   0.048
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      63      5.16       5
     C    5805      2.51       5
     N    1542      2.21       5
     O    1652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9062
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "H"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1785
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2559
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "G"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 396
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 1870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1870
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2347
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 13, 'TRANS': 273}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 76
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.53, per 1000 atoms: 0.94
  Number of scatterers: 9062
  At special positions: 0
  Unit cell: (88.536, 123.69, 130.2, 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      63     16.00
     O    1652      8.00
     N    1542      7.00
     C    5805      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  39 " - pdb=" SG  CYS H 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 176 " - pdb=" SG  CYS H 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 180 " distance=2.04

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 14 sheets defined
      39.5% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'H' and resid 45 through 49
    Processing helix  chain 'H' and resid 79 through 82
    Processing helix  chain 'H' and resid 104 through 108
      removed outlier: 3.645A  pdb=" N   THR H 108 " --> pdb=" O   SER H 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'B' and resid 85 through 87
      No H-bonds generated for 'chain 'B' and resid 85 through 87'
    Processing helix  chain 'G' and resid 13 through 25
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.539A  pdb=" N   ILE A  49 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 246 through 262
      removed outlier: 3.709A  pdb=" N   GLN A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   GLU A 251 " --> pdb=" O   ASN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 266
      removed outlier: 3.707A  pdb=" N   ARG A 266 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 263 through 266'
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 290 through 295
      removed outlier: 3.762A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 4.350A  pdb=" N   ARG A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 335
      removed outlier: 4.001A  pdb=" N   SER A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 374
    Processing helix  chain 'R' and resid 28 through 60
    Processing helix  chain 'R' and resid 66 through 84
      removed outlier: 4.421A  pdb=" N   PHE R  70 " --> pdb=" O   VAL R  66 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 84 through 96
      removed outlier: 4.272A  pdb=" N   HIS R  95 " --> pdb=" O   THR R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 109
    Processing helix  chain 'R' and resid 110 through 136
    Processing helix  chain 'R' and resid 143 through 168
      Proline residue:  R 164  - end of helix
    Processing helix  chain 'R' and resid 190 through 205
      removed outlier: 3.536A  pdb=" N   HIS R 197 " --> pdb=" O   GLU R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 205 through 225
    Processing helix  chain 'R' and resid 238 through 274
      Proline residue:  R 263  - end of helix
      Proline residue:  R 271  - end of helix
    Processing helix  chain 'R' and resid 274 through 279
      removed outlier: 4.158A  pdb=" N   TYR R 278 " --> pdb=" O   ASN R 274 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 296
      removed outlier: 4.165A  pdb=" N   GLN R 285 " --> pdb=" O   LYS R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 296 through 309
      removed outlier: 3.611A  pdb=" N   TYR R 300 " --> pdb=" O   SER R 296 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASN R 301 " --> pdb=" O   SER R 297 " (cutoff:3.500A)
      Proline residue:  R 302  - end of helix
    Processing helix  chain 'R' and resid 309 through 319
      removed outlier: 3.859A  pdb=" N   ARG R 313 " --> pdb=" O   ASN R 309 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 24
    Processing sheet with id=AA2, first strand: chain 'H' and resid 27 through 29
      removed outlier: 6.765A  pdb=" N   MET H  51 " --> pdb=" O   TYR H  67 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   TYR H  67 " --> pdb=" O   MET H  51 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP H  53 " --> pdb=" O   VAL H  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 157 through 158
    Processing sheet with id=AA4, first strand: chain 'H' and resid 163 through 165
      removed outlier: 6.158A  pdb=" N   LEU H 195 " --> pdb=" O   LEU H 204 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   LEU H 204 " --> pdb=" O   LEU H 195 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.452A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.753A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.909A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.548A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.155A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.562A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.248A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 34 through 37
    Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 40
      removed outlier: 7.154A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.166A  pdb=" N   ASP A 242 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   PHE A 239 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ASN A 275 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   VAL A 241 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'R' and resid 169 through 173

    461 hydrogen bonds defined for protein.
    1311 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: 2.98

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1689
        1.32 -     1.45: 2402
        1.45 -     1.57: 5094
        1.57 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 9279
  Sorted by residual:
  bond pdb=" C   VAL B 187 "
       pdb=" N   MET B 188 "
    ideal  model  delta    sigma   weight residual
    1.332  1.439 -0.107 1.36e-02 5.41e+03 6.14e+01
  bond pdb=" CG  ASN R  96 "
       pdb=" OD1 ASN R  96 "
    ideal  model  delta    sigma   weight residual
    1.231  1.323 -0.092 1.90e-02 2.77e+03 2.35e+01
  bond pdb=" N   PHE R 111 "
       pdb=" CA  PHE R 111 "
    ideal  model  delta    sigma   weight residual
    1.463  1.497 -0.033 6.90e-03 2.10e+04 2.34e+01
  bond pdb=" CG  ASN R  96 "
       pdb=" ND2 ASN R  96 "
    ideal  model  delta    sigma   weight residual
    1.328  1.229  0.099 2.10e-02 2.27e+03 2.24e+01
  bond pdb=" C   CYS B 103 "
       pdb=" N   ALA B 104 "
    ideal  model  delta    sigma   weight residual
    1.330  1.268  0.061 1.41e-02 5.03e+03 1.90e+01
  ... (remaining 9274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 10070
        2.01 -     4.02: 2426
        4.02 -     6.03: 90
        6.03 -     8.05: 7
        8.05 -    10.06: 3
  Bond angle restraints: 12596
  Sorted by residual:
  angle pdb=" CA  VAL B 187 "
        pdb=" C   VAL B 187 "
        pdb=" N   MET B 188 "
      ideal   model   delta    sigma   weight residual
     116.33  125.15   -8.82 1.03e+00 9.43e-01 7.33e+01
  angle pdb=" N   ASP B 154 "
        pdb=" CA  ASP B 154 "
        pdb=" C   ASP B 154 "
      ideal   model   delta    sigma   weight residual
     113.02  103.88    9.14 1.20e+00 6.94e-01 5.81e+01
  angle pdb=" C   HIS B 311 "
        pdb=" N   ASP B 312 "
        pdb=" CA  ASP B 312 "
      ideal   model   delta    sigma   weight residual
     122.60  112.54   10.06 1.56e+00 4.11e-01 4.16e+01
  angle pdb=" O   VAL B 187 "
        pdb=" C   VAL B 187 "
        pdb=" N   MET B 188 "
      ideal   model   delta    sigma   weight residual
     122.66  116.62    6.04 1.07e+00 8.73e-01 3.19e+01
  angle pdb=" N   LEU B 152 "
        pdb=" CA  LEU B 152 "
        pdb=" C   LEU B 152 "
      ideal   model   delta    sigma   weight residual
     112.68  105.34    7.34 1.33e+00 5.65e-01 3.04e+01
  ... (remaining 12591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 5129
       16.70 -    33.39: 309
       33.39 -    50.09: 64
       50.09 -    66.79: 21
       66.79 -    83.48: 3
  Dihedral angle restraints: 5526
    sinusoidal: 2202
      harmonic: 3324
  Sorted by residual:
  dihedral pdb=" CB  CYS H  39 "
           pdb=" SG  CYS H  39 "
           pdb=" SG  CYS H 113 "
           pdb=" CB  CYS H 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.66   32.34     1      1.00e+01 1.00e-02 1.49e+01
  dihedral pdb=" C   PHE B 151 "
           pdb=" N   PHE B 151 "
           pdb=" CA  PHE B 151 "
           pdb=" CB  PHE B 151 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.69   -8.91     0      2.50e+00 1.60e-01 1.27e+01
  dihedral pdb=" CA  TYR H 252 "
           pdb=" C   TYR H 252 "
           pdb=" N   PRO H 253 "
           pdb=" CA  PRO H 253 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   17.10  -17.10     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 5523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 459
       0.053 -    0.106: 451
       0.106 -    0.158: 334
       0.158 -    0.211: 136
       0.211 -    0.264: 27
  Chirality restraints: 1407
  Sorted by residual:
  chirality pdb=" CB  VAL R 126 "
            pdb=" CA  VAL R 126 "
            pdb=" CG1 VAL R 126 "
            pdb=" CG2 VAL R 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  ILE B 120 "
            pdb=" N   ILE B 120 "
            pdb=" C   ILE B 120 "
            pdb=" CB  ILE B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  LEU B  79 "
            pdb=" N   LEU B  79 "
            pdb=" C   LEU B  79 "
            pdb=" CB  LEU B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1404 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 103 "    0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   CYS B 103 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   CYS B 103 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B 104 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 245 "   -0.011 2.00e-02 2.50e+03   2.34e-02 5.48e+00
        pdb=" C   ASP A 245 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASP A 245 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TYR A 246 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 196 "    0.008 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" C   THR B 196 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   THR B 196 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B 197 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 52
        2.65 -     3.21: 8532
        3.21 -     3.77: 14544
        3.77 -     4.34: 21309
        4.34 -     4.90: 33245
  Nonbonded interactions: 77682
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" CD2 PHE R  70 "
            pdb=" OD2 ASP R 129 "
     model   vdw
     2.209 3.340
  nonbonded pdb=" N   ASP B 154 "
            pdb=" N   ASN B 155 "
     model   vdw
     2.506 2.560
  nonbonded pdb=" O   THR H 161 "
            pdb=" OG1 THR H 260 "
     model   vdw
     2.520 3.040
  nonbonded pdb=" N   CYS B 166 "
            pdb=" O   CYS B 166 "
     model   vdw
     2.561 2.496
  ... (remaining 77677 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:             61.850
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.940
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:14.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  104.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
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      :  0.012   0.107   9279  Z= 0.804
  Angle     :  1.511  10.057  12596  Z= 1.178
  Chirality :  0.103   0.264   1407
  Planarity :  0.004   0.036   1587
  Dihedral  : 11.726  83.483   3373
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.05 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.23), residues: 1120
  helix: -0.91 (0.24), residues: 378
  sheet: -0.86 (0.31), residues: 236
  loop : -1.34 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.009   0.002   HIS B 311 
 PHE   0.021   0.002   PHE B 151 
 TYR   0.023   0.002   TYR H 207 
 ARG   0.006   0.001   ARG R 177 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 256
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   63 GLU cc_start: 0.7576 (tt0) cc_final: 0.7325 (tm-30)
REVERT: B  155 ASN cc_start: 0.7592 (t0) cc_final: 0.7196 (t0)
REVERT: B  263 THR cc_start: 0.8886 (t) cc_final: 0.8659 (m)
REVERT: A    6 SER cc_start: 0.8271 (p) cc_final: 0.7890 (p)
REVERT: A    8 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7688 (mm-30)
REVERT: A    9 ASP cc_start: 0.7798 (m-30) cc_final: 0.7434 (m-30)
REVERT: A   17 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7326 (mtpt)
REVERT: A  263 ARG cc_start: 0.7061 (ptm160) cc_final: 0.6829 (ptm160)
REVERT: A  368 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6937 (mtt-85)
REVERT: A  372 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6756 (tpt-90)
REVERT: R   51 VAL cc_start: 0.7563 (t) cc_final: 0.7154 (p)
REVERT: R   63 MET cc_start: 0.6860 (mmm) cc_final: 0.6296 (mtt)
REVERT: R  109 ASN cc_start: 0.6708 (m-40) cc_final: 0.6060 (m-40)
REVERT: R  161 LEU cc_start: 0.7349 (tp) cc_final: 0.7079 (tt)
REVERT: R  163 PHE cc_start: 0.6569 (t80) cc_final: 0.6198 (t80)
REVERT: R  182 ILE cc_start: 0.7803 (mt) cc_final: 0.7453 (mp)
REVERT: P    8 PHE cc_start: 0.8219 (m-80) cc_final: 0.7845 (m-10)
  outliers start: 11
  outliers final: 2
  residues processed: 266
  average time/residue: 1.4507
  time to fit residues: 413.2186
Evaluate side-chains
  176 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 173
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  172 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain A residue  368 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  99 GLN
B  17 GLN
B 266 HIS
A 206 GLN
A 211 ASN
R  50 ASN
R  68 ASN
R 274 ASN
R 301 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.183528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125935 restraints weight = 10060.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.21
r_work: 0.3209 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9279  Z= 0.213
  Angle     :  0.595   7.228  12596  Z= 0.320
  Chirality :  0.044   0.148   1407
  Planarity :  0.004   0.049   1587
  Dihedral  :  4.490  48.606   1317
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.32 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.04 (0.24), residues: 1120
  helix:  1.46 (0.25), residues: 390
  sheet: -0.86 (0.29), residues: 246
  loop : -0.59 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.010   0.001   HIS A 213 
 PHE   0.024   0.002   PHE H  85 
 TYR   0.020   0.002   TYR R 272 
 ARG   0.006   0.001   ARG A 339 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 205
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  106 GLU cc_start: 0.8594 (mp0) cc_final: 0.8372 (mt-10)
REVERT: H  180 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7960 (ttpp)
REVERT: H  208 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7093 (mtp180)
REVERT: B  155 ASN cc_start: 0.8220 (t0) cc_final: 0.7499 (t0)
REVERT: B  195 ASP cc_start: 0.7282 (p0) cc_final: 0.6985 (p0)
REVERT: B  197 ARG cc_start: 0.7218 (mmt180) cc_final: 0.6966 (mmp-170)
REVERT: B  219 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7964 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8260 (mp0)
REVERT: B  263 THR cc_start: 0.8924 (t) cc_final: 0.8715 (m)
REVERT: G   18 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6542 (tm-30)
REVERT: A   17 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7309 (mtpt)
REVERT: A  206 GLN cc_start: 0.7279 (tt0) cc_final: 0.6941 (tm-30)
REVERT: A  263 ARG cc_start: 0.7170 (ptm160) cc_final: 0.6884 (ttp-110)
REVERT: A  326 ASP cc_start: 0.7480 (t0) cc_final: 0.7250 (t70)
REVERT: A  368 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6801 (mtt180)
REVERT: A  369 MET cc_start: 0.7250 (ttm) cc_final: 0.7036 (ttt)
REVERT: A  372 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6349 (tpp-160)
REVERT: R   63 MET cc_start: 0.6537 (mmm) cc_final: 0.6022 (mtt)
REVERT: R   90 PHE cc_start: 0.8663 (t80) cc_final: 0.8423 (t80)
REVERT: R  109 ASN cc_start: 0.5833 (m-40) cc_final: 0.5579 (m-40)
REVERT: R  121 TYR cc_start: 0.7377 (m-80) cc_final: 0.7166 (m-80)
REVERT: R  161 LEU cc_start: 0.7058 (tp) cc_final: 0.6724 (tt)
REVERT: R  163 PHE cc_start: 0.6529 (t80) cc_final: 0.6161 (t80)
REVERT: R  305 TYR cc_start: 0.6574 (m-10) cc_final: 0.6371 (m-10)
REVERT: P    8 PHE cc_start: 0.8151 (m-80) cc_final: 0.7704 (m-10)
  outliers start: 31
  outliers final: 14
  residues processed: 227
  average time/residue: 1.2310
  time to fit residues: 298.5241
Evaluate side-chains
  190 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  172 VAL
Chi-restraints excluded: chain H residue  208 ARG
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   18 GLN
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  295 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 13 optimal weight:   20.0000
   chunk 31 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0770
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.8540

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

Flipped N/Q/H residues before XYZ refinement:
H  99 GLN
B  17 GLN
A 277 GLN
R  50 ASN
R  96 ASN
R 136 HIS
R 274 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.183084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125643 restraints weight = 10125.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.11
r_work: 0.3180 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9279  Z= 0.226
  Angle     :  0.577   8.779  12596  Z= 0.307
  Chirality :  0.044   0.255   1407
  Planarity :  0.004   0.043   1587
  Dihedral  :  4.495  49.387   1316
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 16.96 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.32 (0.24), residues: 1120
  helix:  1.79 (0.25), residues: 385
  sheet: -0.71 (0.28), residues: 261
  loop : -0.46 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.033   0.002   PHE H  85 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.007   0.000   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   80 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (p)
REVERT: H  106 GLU cc_start: 0.8585 (mp0) cc_final: 0.8370 (mt-10)
REVERT: H  208 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.6917 (mtp180)
REVERT: B   52 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8141 (mtt90)
REVERT: B  155 ASN cc_start: 0.8373 (t0) cc_final: 0.7852 (t0)
REVERT: B  217 MET cc_start: 0.8279 (pmt) cc_final: 0.8067 (pmm)
REVERT: B  219 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7832 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8324 (mp0)
REVERT: B  263 THR cc_start: 0.9004 (t) cc_final: 0.8753 (m)
REVERT: G   20 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7906 (mptm)
REVERT: A   17 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7349 (mtpt)
REVERT: A   21 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7494 (mtmm)
REVERT: A  206 GLN cc_start: 0.7249 (tt0) cc_final: 0.6885 (tm-30)
REVERT: A  254 ASN cc_start: 0.8158 (m-40) cc_final: 0.7918 (m110)
REVERT: A  263 ARG cc_start: 0.7193 (ptm160) cc_final: 0.6927 (ttp-110)
REVERT: A  290 LYS cc_start: 0.8237 (mppt) cc_final: 0.7968 (mptt)
REVERT: A  326 ASP cc_start: 0.7565 (t0) cc_final: 0.7278 (t70)
REVERT: A  372 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6967 (mtm110)
REVERT: R   63 MET cc_start: 0.6523 (mmm) cc_final: 0.6087 (mtt)
REVERT: R   81 MET cc_start: 0.7412 (ttm) cc_final: 0.7164 (ptp)
REVERT: R  161 LEU cc_start: 0.7060 (tp) cc_final: 0.6707 (tt)
REVERT: R  163 PHE cc_start: 0.6514 (t80) cc_final: 0.6160 (t80)
REVERT: R  205 TYR cc_start: 0.7786 (t80) cc_final: 0.6833 (t80)
REVERT: P    8 PHE cc_start: 0.8234 (m-80) cc_final: 0.7788 (m-10)
  outliers start: 39
  outliers final: 19
  residues processed: 192
  average time/residue: 1.3356
  time to fit residues: 274.0681
Evaluate side-chains
  173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  172 VAL
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain H residue  203 GLN
Chi-restraints excluded: chain H residue  208 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain R residue   72 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0970
   chunk 61 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
A  22 GLN
A 277 GLN
R 301 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.184935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.128108 restraints weight = 10026.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.30
r_work: 0.3159 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9279  Z= 0.182
  Angle     :  0.532   7.749  12596  Z= 0.284
  Chirality :  0.042   0.141   1407
  Planarity :  0.004   0.041   1587
  Dihedral  :  4.077  26.636   1312
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.36 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.51 (0.24), residues: 1120
  helix:  1.91 (0.25), residues: 388
  sheet: -0.74 (0.28), residues: 274
  loop : -0.22 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.030   0.002   PHE R  90 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 173
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   80 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8604 (p)
REVERT: H  106 GLU cc_start: 0.8632 (mp0) cc_final: 0.8395 (mt-10)
REVERT: B  155 ASN cc_start: 0.8420 (t0) cc_final: 0.8121 (t0)
REVERT: B  217 MET cc_start: 0.8281 (pmt) cc_final: 0.8027 (pmm)
REVERT: B  219 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7799 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8301 (mp0)
REVERT: B  247 ASP cc_start: 0.7756 (t0) cc_final: 0.7320 (t0)
REVERT: B  263 THR cc_start: 0.8981 (t) cc_final: 0.8722 (m)
REVERT: G   20 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7891 (mptm)
REVERT: A   17 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7332 (mtpt)
REVERT: A   21 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7434 (mtmm)
REVERT: A  206 GLN cc_start: 0.7256 (tt0) cc_final: 0.6864 (tm-30)
REVERT: A  254 ASN cc_start: 0.8146 (m-40) cc_final: 0.7879 (m110)
REVERT: A  263 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6861 (ttp-110)
REVERT: A  290 LYS cc_start: 0.8301 (mppt) cc_final: 0.8045 (mptp)
REVERT: A  326 ASP cc_start: 0.7625 (t0) cc_final: 0.7331 (t70)
REVERT: A  368 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6827 (mtt180)
REVERT: R   63 MET cc_start: 0.6437 (mmm) cc_final: 0.6083 (mtt)
REVERT: R   85 ASN cc_start: 0.6334 (t0) cc_final: 0.5793 (t160)
REVERT: R   89 ASN cc_start: 0.7275 (m-40) cc_final: 0.6618 (m-40)
REVERT: R  161 LEU cc_start: 0.7078 (tp) cc_final: 0.6764 (tt)
REVERT: R  163 PHE cc_start: 0.6472 (t80) cc_final: 0.6119 (t80)
REVERT: R  205 TYR cc_start: 0.7809 (t80) cc_final: 0.6786 (t80)
REVERT: R  262 LEU cc_start: 0.7618 (tp) cc_final: 0.7187 (tp)
REVERT: P    8 PHE cc_start: 0.8275 (m-80) cc_final: 0.7831 (m-10)
  outliers start: 42
  outliers final: 15
  residues processed: 204
  average time/residue: 1.2305
  time to fit residues: 268.3220
Evaluate side-chains
  179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  100 TYR
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 84 optimal weight:   10.0000
   chunk 98 optimal weight:   40.0000
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
H  30 GLN
H 196 GLN
B  17 GLN
B 259 GLN
A 213 HIS
A 229 GLN
A 277 GLN
R  50 ASN
R  68 ASN
R  96 ASN
R 274 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.180008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.121955 restraints weight = 10071.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.15
r_work: 0.3096 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9279  Z= 0.360
  Angle     :  0.624   9.812  12596  Z= 0.328
  Chirality :  0.045   0.165   1407
  Planarity :  0.004   0.038   1587
  Dihedral  :  4.383  28.322   1311
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 17.98 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.24), residues: 1120
  helix:  1.67 (0.25), residues: 384
  sheet: -0.68 (0.28), residues: 281
  loop : -0.27 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 345 
 PHE   0.035   0.002   PHE H  85 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.008   0.000   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 171
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: H  106 GLU cc_start: 0.8605 (mp0) cc_final: 0.8374 (mt-10)
REVERT: B  155 ASN cc_start: 0.8542 (t0) cc_final: 0.8127 (t0)
REVERT: B  176 GLN cc_start: 0.8581 (mt0) cc_final: 0.8368 (tt0)
REVERT: B  217 MET cc_start: 0.8359 (pmt) cc_final: 0.8085 (pmm)
REVERT: B  219 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7863 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8290 (mp0)
REVERT: B  258 ASP cc_start: 0.8171 (t0) cc_final: 0.7740 (t70)
REVERT: B  273 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (mp)
REVERT: G   20 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7907 (mptm)
REVERT: A   17 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7442 (mtpt)
REVERT: A   21 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7513 (mtmm)
REVERT: A   26 ASP cc_start: 0.8183 (m-30) cc_final: 0.7626 (m-30)
REVERT: A  206 GLN cc_start: 0.7253 (tt0) cc_final: 0.6921 (tm-30)
REVERT: A  229 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8332 (pp30)
REVERT: A  290 LYS cc_start: 0.8481 (mppt) cc_final: 0.8224 (mptp)
REVERT: A  326 ASP cc_start: 0.7666 (t0) cc_final: 0.7371 (t70)
REVERT: A  368 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6827 (mtt180)
REVERT: R   63 MET cc_start: 0.6548 (mmm) cc_final: 0.6199 (mtt)
REVERT: R   68 ASN cc_start: 0.7841 (m-40) cc_final: 0.7638 (m110)
REVERT: R   89 ASN cc_start: 0.7347 (m-40) cc_final: 0.6702 (m-40)
REVERT: R  161 LEU cc_start: 0.7078 (tp) cc_final: 0.6763 (tp)
REVERT: R  163 PHE cc_start: 0.6561 (t80) cc_final: 0.6227 (t80)
REVERT: R  205 TYR cc_start: 0.7818 (t80) cc_final: 0.6777 (t80)
REVERT: R  262 LEU cc_start: 0.7736 (tp) cc_final: 0.7296 (tp)
REVERT: P    8 PHE cc_start: 0.8304 (m-80) cc_final: 0.7992 (m-80)
  outliers start: 49
  outliers final: 21
  residues processed: 203
  average time/residue: 1.1396
  time to fit residues: 248.1435
Evaluate side-chains
  188 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  166 VAL
Chi-restraints excluded: chain H residue  203 GLN
Chi-restraints excluded: chain H residue  223 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  100 TYR
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 91 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
A 277 GLN
R  50 ASN
R  96 ASN
R 274 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.181391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126365 restraints weight = 10004.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.17
r_work: 0.3109 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9279  Z= 0.271
  Angle     :  0.573   9.356  12596  Z= 0.304
  Chirality :  0.044   0.158   1407
  Planarity :  0.004   0.038   1587
  Dihedral  :  4.313  26.606   1311
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.20 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.39 (0.24), residues: 1120
  helix:  1.72 (0.25), residues: 387
  sheet: -0.71 (0.28), residues: 285
  loop : -0.25 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.043   0.002   PHE H  85 
 TYR   0.015   0.002   TYR B  59 
 ARG   0.007   0.000   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 168
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   80 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8723 (p)
REVERT: H  106 GLU cc_start: 0.8600 (mp0) cc_final: 0.8378 (mt-10)
REVERT: B  155 ASN cc_start: 0.8543 (t0) cc_final: 0.8148 (t0)
REVERT: B  176 GLN cc_start: 0.8545 (mt0) cc_final: 0.8327 (tt0)
REVERT: B  217 MET cc_start: 0.8395 (pmt) cc_final: 0.8134 (pmm)
REVERT: B  219 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7869 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8294 (mp0)
REVERT: B  258 ASP cc_start: 0.8133 (t0) cc_final: 0.7674 (t70)
REVERT: G   18 GLN cc_start: 0.7371 (mm-40) cc_final: 0.6925 (tm-30)
REVERT: G   20 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7906 (mptm)
REVERT: A   17 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7446 (mtpt)
REVERT: A   21 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7492 (mtmm)
REVERT: A   26 ASP cc_start: 0.8150 (m-30) cc_final: 0.7577 (m-30)
REVERT: A  206 GLN cc_start: 0.7220 (tt0) cc_final: 0.6914 (tm-30)
REVERT: A  213 HIS cc_start: 0.7926 (t70) cc_final: 0.7706 (m-70)
REVERT: A  229 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8287 (pp30)
REVERT: A  290 LYS cc_start: 0.8519 (mppt) cc_final: 0.8258 (mptp)
REVERT: A  326 ASP cc_start: 0.7719 (t0) cc_final: 0.7432 (t70)
REVERT: A  368 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6841 (mtt180)
REVERT: R   63 MET cc_start: 0.6548 (mmm) cc_final: 0.6235 (mtt)
REVERT: R   89 ASN cc_start: 0.7329 (m-40) cc_final: 0.6741 (m-40)
REVERT: R  161 LEU cc_start: 0.7099 (tp) cc_final: 0.6833 (tp)
REVERT: R  163 PHE cc_start: 0.6533 (t80) cc_final: 0.6203 (t80)
REVERT: R  205 TYR cc_start: 0.7841 (t80) cc_final: 0.6819 (t80)
REVERT: R  299 MET cc_start: 0.7428 (ptm) cc_final: 0.6848 (ptt)
REVERT: R  300 TYR cc_start: 0.6351 (m-10) cc_final: 0.5840 (m-10)
REVERT: R  314 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5889 (mt)
REVERT: P    8 PHE cc_start: 0.8334 (m-80) cc_final: 0.8000 (m-80)
  outliers start: 41
  outliers final: 22
  residues processed: 197
  average time/residue: 1.3539
  time to fit residues: 286.0362
Evaluate side-chains
  185 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  166 VAL
Chi-restraints excluded: chain H residue  223 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  100 TYR
Chi-restraints excluded: chain R residue  207 LEU
Chi-restraints excluded: chain R residue  314 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
A 250 GLN
A 254 ASN
A 275 ASN
A 277 GLN
R  68 ASN
R  96 ASN
R 274 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.179911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.121921 restraints weight = 10169.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.13
r_work: 0.3099 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9279  Z= 0.352
  Angle     :  0.611  10.057  12596  Z= 0.324
  Chirality :  0.045   0.217   1407
  Planarity :  0.004   0.037   1587
  Dihedral  :  4.459  27.092   1311
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 18.59 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.35 (0.24), residues: 1120
  helix:  1.59 (0.25), residues: 384
  sheet: -0.57 (0.29), residues: 267
  loop : -0.32 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.045   0.002   PHE H  85 
 TYR   0.017   0.002   TYR R 305 
 ARG   0.007   0.001   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 160
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  106 GLU cc_start: 0.8650 (mp0) cc_final: 0.8406 (mt-10)
REVERT: H  208 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.6971 (mtp180)
REVERT: B  155 ASN cc_start: 0.8589 (t0) cc_final: 0.8200 (t0)
REVERT: B  176 GLN cc_start: 0.8544 (mt0) cc_final: 0.8334 (tt0)
REVERT: B  258 ASP cc_start: 0.8147 (t0) cc_final: 0.7788 (t70)
REVERT: G   20 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7923 (mptm)
REVERT: A   17 LYS cc_start: 0.8290 (mmtp) cc_final: 0.7480 (mtpt)
REVERT: A   21 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7541 (mtmm)
REVERT: A   26 ASP cc_start: 0.8119 (m-30) cc_final: 0.7514 (m-30)
REVERT: A  206 GLN cc_start: 0.7190 (tt0) cc_final: 0.6867 (tm-30)
REVERT: A  229 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8101 (pp30)
REVERT: A  290 LYS cc_start: 0.8588 (mppt) cc_final: 0.8359 (mptp)
REVERT: A  326 ASP cc_start: 0.7721 (t0) cc_final: 0.7434 (t70)
REVERT: A  368 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6803 (mtt180)
REVERT: R   63 MET cc_start: 0.6572 (mmm) cc_final: 0.6230 (mtt)
REVERT: R   89 ASN cc_start: 0.7410 (m-40) cc_final: 0.6813 (m-40)
REVERT: R  161 LEU cc_start: 0.7112 (tp) cc_final: 0.6858 (tp)
REVERT: R  163 PHE cc_start: 0.6552 (t80) cc_final: 0.6268 (t80)
REVERT: R  205 TYR cc_start: 0.7812 (t80) cc_final: 0.6754 (t80)
REVERT: R  299 MET cc_start: 0.7460 (ptm) cc_final: 0.7234 (ptm)
REVERT: R  300 TYR cc_start: 0.6344 (m-10) cc_final: 0.6069 (m-10)
REVERT: R  314 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5831 (mt)
REVERT: P    8 PHE cc_start: 0.8281 (m-80) cc_final: 0.7955 (m-80)
  outliers start: 44
  outliers final: 26
  residues processed: 194
  average time/residue: 1.3775
  time to fit residues: 285.5004
Evaluate side-chains
  187 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 1.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   23 GLU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  166 VAL
Chi-restraints excluded: chain H residue  172 VAL
Chi-restraints excluded: chain H residue  203 GLN
Chi-restraints excluded: chain H residue  208 ARG
Chi-restraints excluded: chain H residue  223 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  100 TYR
Chi-restraints excluded: chain R residue  266 ILE
Chi-restraints excluded: chain R residue  314 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  59 ASN
A 275 ASN
A 277 GLN
R  68 ASN
R  96 ASN
R 274 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.182234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.124637 restraints weight = 10186.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.13
r_work: 0.3139 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9279  Z= 0.220
  Angle     :  0.569  10.236  12596  Z= 0.299
  Chirality :  0.043   0.198   1407
  Planarity :  0.004   0.037   1587
  Dihedral  :  4.279  24.809   1311
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.82 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.53 (0.25), residues: 1120
  helix:  1.77 (0.25), residues: 382
  sheet: -0.54 (0.29), residues: 271
  loop : -0.17 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.032   0.001   PHE H  85 
 TYR   0.016   0.002   TYR R 305 
 ARG   0.008   0.000   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: H   63 GLU cc_start: 0.8485 (tt0) cc_final: 0.7814 (pt0)
REVERT: H   80 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8697 (p)
REVERT: H  106 GLU cc_start: 0.8612 (mp0) cc_final: 0.8373 (mt-10)
REVERT: H  208 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8793 (mtt90)
REVERT: B  155 ASN cc_start: 0.8545 (t0) cc_final: 0.8294 (t0)
REVERT: B  219 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7841 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8162 (mp0)
REVERT: B  258 ASP cc_start: 0.8056 (t0) cc_final: 0.7610 (t70)
REVERT: B  263 THR cc_start: 0.9090 (t) cc_final: 0.8730 (m)
REVERT: A   17 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7450 (mtpt)
REVERT: A   21 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7440 (mtmm)
REVERT: A   26 ASP cc_start: 0.8060 (m-30) cc_final: 0.7478 (m-30)
REVERT: A  206 GLN cc_start: 0.7146 (tt0) cc_final: 0.6845 (tm-30)
REVERT: A  213 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7384 (t-170)
REVERT: A  229 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8206 (pp30)
REVERT: A  290 LYS cc_start: 0.8562 (mppt) cc_final: 0.8018 (ttpp)
REVERT: A  326 ASP cc_start: 0.7707 (t0) cc_final: 0.7428 (t70)
REVERT: A  368 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6836 (mtt-85)
REVERT: R   63 MET cc_start: 0.6515 (mmm) cc_final: 0.6242 (mtt)
REVERT: R   85 ASN cc_start: 0.6460 (t0) cc_final: 0.5885 (t160)
REVERT: R   89 ASN cc_start: 0.7311 (m-40) cc_final: 0.6662 (m-40)
REVERT: R  161 LEU cc_start: 0.7102 (tp) cc_final: 0.6879 (tp)
REVERT: R  163 PHE cc_start: 0.6556 (t80) cc_final: 0.6243 (t80)
REVERT: R  205 TYR cc_start: 0.7826 (t80) cc_final: 0.6762 (t80)
REVERT: R  299 MET cc_start: 0.7451 (ptm) cc_final: 0.7239 (ptm)
REVERT: R  300 TYR cc_start: 0.6266 (m-10) cc_final: 0.6057 (m-10)
REVERT: R  314 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5881 (mt)
REVERT: P    8 PHE cc_start: 0.8311 (m-80) cc_final: 0.8029 (m-80)
  outliers start: 33
  outliers final: 21
  residues processed: 186
  average time/residue: 1.2216
  time to fit residues: 242.9316
Evaluate side-chains
  185 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  166 VAL
Chi-restraints excluded: chain H residue  203 GLN
Chi-restraints excluded: chain H residue  208 ARG
Chi-restraints excluded: chain H residue  223 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  100 TYR
Chi-restraints excluded: chain R residue  266 ILE
Chi-restraints excluded: chain R residue  314 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 109 optimal weight:    0.4980
   chunk 13 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H  56 GLN
H 196 GLN
B  17 GLN
B 176 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 ASN
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R  96 ASN
R 274 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.182454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124620 restraints weight = 9980.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.14
r_work: 0.3159 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9279  Z= 0.229
  Angle     :  0.583  12.921  12596  Z= 0.302
  Chirality :  0.043   0.188   1407
  Planarity :  0.004   0.039   1587
  Dihedral  :  4.249  24.905   1311
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.71 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.54 (0.25), residues: 1120
  helix:  1.70 (0.25), residues: 385
  sheet: -0.41 (0.29), residues: 279
  loop : -0.17 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.030   0.001   PHE H  85 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.011   0.000   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: H   60 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8692 (mppt)
REVERT: H   63 GLU cc_start: 0.8488 (tt0) cc_final: 0.7851 (pt0)
REVERT: H   80 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8696 (p)
REVERT: H  106 GLU cc_start: 0.8610 (mp0) cc_final: 0.8376 (mt-10)
REVERT: H  208 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8809 (mtt90)
REVERT: B  155 ASN cc_start: 0.8549 (t0) cc_final: 0.8301 (t0)
REVERT: B  219 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7824 (mmm-85)
REVERT: B  226 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8146 (mp0)
REVERT: B  258 ASP cc_start: 0.8021 (t0) cc_final: 0.7613 (t70)
REVERT: B  263 THR cc_start: 0.9038 (t) cc_final: 0.8716 (m)
REVERT: A   17 LYS cc_start: 0.8274 (mmtp) cc_final: 0.7454 (mtpt)
REVERT: A   26 ASP cc_start: 0.8081 (m-30) cc_final: 0.7489 (m-30)
REVERT: A  206 GLN cc_start: 0.7180 (tt0) cc_final: 0.6866 (tm-30)
REVERT: A  213 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7343 (t-170)
REVERT: A  229 GLN cc_start: 0.8601 (tm-30) cc_final: 0.7832 (pp30)
REVERT: A  290 LYS cc_start: 0.8609 (mppt) cc_final: 0.8071 (ttpp)
REVERT: A  326 ASP cc_start: 0.7673 (t0) cc_final: 0.7402 (t70)
REVERT: A  368 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6818 (mtt-85)
REVERT: R   63 MET cc_start: 0.6516 (mmm) cc_final: 0.6274 (mtt)
REVERT: R   85 ASN cc_start: 0.6487 (t0) cc_final: 0.5952 (t160)
REVERT: R   89 ASN cc_start: 0.7288 (m-40) cc_final: 0.6758 (m-40)
REVERT: R  163 PHE cc_start: 0.6552 (t80) cc_final: 0.6284 (t80)
REVERT: R  205 TYR cc_start: 0.7833 (t80) cc_final: 0.6771 (t80)
REVERT: R  299 MET cc_start: 0.7515 (ptm) cc_final: 0.7299 (ptm)
REVERT: R  314 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5867 (mt)
REVERT: P    8 PHE cc_start: 0.8307 (m-80) cc_final: 0.8030 (m-80)
  outliers start: 32
  outliers final: 20
  residues processed: 188
  average time/residue: 1.1931
  time to fit residues: 239.6412
Evaluate side-chains
  186 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  166 VAL
Chi-restraints excluded: chain H residue  172 VAL
Chi-restraints excluded: chain H residue  203 GLN
Chi-restraints excluded: chain H residue  208 ARG
Chi-restraints excluded: chain H residue  223 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  266 ILE
Chi-restraints excluded: chain R residue  314 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0570
   chunk 23 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
H  56 GLN
H 196 GLN
B  17 GLN
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
A 275 ASN
A 277 GLN
R  68 ASN
R  73 ASN
** R  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 274 ASN
** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.179371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.120970 restraints weight = 10025.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.13
r_work: 0.3087 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9279  Z= 0.397
  Angle     :  0.669  13.471  12596  Z= 0.348
  Chirality :  0.047   0.205   1407
  Planarity :  0.004   0.043   1587
  Dihedral  :  4.553  26.885   1311
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.02 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.45 (0.25), residues: 1120
  helix:  1.54 (0.25), residues: 379
  sheet: -0.37 (0.29), residues: 272
  loop : -0.20 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.011   0.002   HIS B 266 
 PHE   0.040   0.002   PHE H  85 
 TYR   0.024   0.002   TYR R 305 
 ARG   0.013   0.001   ARG B  19 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: H   63 GLU cc_start: 0.8559 (tt0) cc_final: 0.7903 (pt0)
REVERT: H  106 GLU cc_start: 0.8650 (mp0) cc_final: 0.8396 (mt-10)
REVERT: H  208 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.6911 (mtp180)
REVERT: B  155 ASN cc_start: 0.8607 (t0) cc_final: 0.8212 (t0)
REVERT: B  219 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7835 (mmm-85)
REVERT: B  258 ASP cc_start: 0.8175 (t0) cc_final: 0.7901 (t0)
REVERT: A   17 LYS cc_start: 0.8366 (mmtp) cc_final: 0.7571 (mtpt)
REVERT: A   26 ASP cc_start: 0.8117 (m-30) cc_final: 0.7516 (m-30)
REVERT: A  206 GLN cc_start: 0.7176 (tt0) cc_final: 0.6845 (tm-30)
REVERT: A  213 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7400 (t-170)
REVERT: A  229 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8479 (pp30)
REVERT: A  290 LYS cc_start: 0.8664 (mppt) cc_final: 0.8114 (ttpp)
REVERT: A  326 ASP cc_start: 0.7722 (t0) cc_final: 0.7443 (t70)
REVERT: A  368 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6795 (mtt180)
REVERT: R   63 MET cc_start: 0.6550 (mmm) cc_final: 0.6294 (mtt)
REVERT: R   89 ASN cc_start: 0.7240 (m-40) cc_final: 0.6648 (m-40)
REVERT: R  163 PHE cc_start: 0.6628 (t80) cc_final: 0.6358 (t80)
REVERT: R  205 TYR cc_start: 0.7849 (t80) cc_final: 0.6782 (t80)
REVERT: R  300 TYR cc_start: 0.6279 (m-10) cc_final: 0.6043 (m-10)
REVERT: R  314 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5840 (mt)
REVERT: P    8 PHE cc_start: 0.8285 (m-80) cc_final: 0.8012 (m-80)
  outliers start: 32
  outliers final: 18
  residues processed: 181
  average time/residue: 1.1342
  time to fit residues: 220.3637
Evaluate side-chains
  172 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   72 SER
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  172 VAL
Chi-restraints excluded: chain H residue  203 GLN
Chi-restraints excluded: chain H residue  208 ARG
Chi-restraints excluded: chain H residue  223 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  266 ILE
Chi-restraints excluded: chain R residue  314 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    0.0670
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 47 optimal weight:    0.3980
   chunk 105 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
H  56 GLN
B  17 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
G  59 ASN
A 229 GLN
A 275 ASN
A 277 GLN
R  68 ASN
** R  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 274 ASN
** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.181384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123678 restraints weight = 10022.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.13
r_work: 0.3157 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9279  Z= 0.195
  Angle     :  0.608  12.173  12596  Z= 0.313
  Chirality :  0.044   0.187   1407
  Planarity :  0.004   0.039   1587
  Dihedral  :  4.317  23.969   1311
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 21.55 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1120
  helix:  1.64 (0.25), residues: 382
  sheet: -0.43 (0.29), residues: 280
  loop : -0.06 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.021   0.001   PHE H  85 
 TYR   0.028   0.002   TYR R 300 
 ARG   0.012   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9133.81 seconds
wall clock time: 160 minutes 54.36 seconds (9654.36 seconds total)