Starting phenix.real_space_refine
on Fri Dec  8 06:37:35 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/12_2023/8gbj_29917_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/12_2023/8gbj_29917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/12_2023/8gbj_29917.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/12_2023/8gbj_29917.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/12_2023/8gbj_29917_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/12_2023/8gbj_29917_updated.pdb"
  }
  resolution = 3.11
  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=   0.000 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      15      5.49       5
     S      50      5.16       5
     C    4685      2.51       5
     N    1296      2.21       5
     O    1421      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B GLU   51": "OE1" <-> "OE2"
    Residue "C GLU   37": "OE1" <-> "OE2"
    Residue "C GLU   92": "OE1" <-> "OE2"
    Residue "C PHE   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  197": "OE1" <-> "OE2"
    Residue "C GLU  232": "OE1" <-> "OE2"
    Residue "C GLU  303": "OE1" <-> "OE2"
    Residue "C TYR  327": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  348": "OD1" <-> "OD2"
    Residue "D ASP  174": "OD1" <-> "OD2"
    Residue "D ASP  180": "OD1" <-> "OD2"
    Residue "D GLU  184": "OE1" <-> "OE2"
    Residue "X GLU   26": "OE1" <-> "OE2"
    Residue "X GLU   75": "OE1" <-> "OE2"
    Residue "X PHE  116": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X GLU  134": "OE1" <-> "OE2"
    Residue "X GLU  164": "OE1" <-> "OE2"
    Residue "X TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7467
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 570
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 2494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2494
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 11, 'TRANS': 305}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2318
          Classifications: {'peptide': 308}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 299}
          Chain breaks: 2
    Chain: "X"
      Number of atoms: 1878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1878
          Classifications: {'peptide': 232}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 225}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 114
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    Chain: "C"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "X"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.38, per 1000 atoms: 0.59
  Number of scatterers: 7467
  At special positions: 0
  Unit cell: (84.39, 81.78, 112.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     P      15     15.00
     O    1421      8.00
     N    1296      7.00
     C    4685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  27 " - pdb=" SG  CYS B  60 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      43 helices and 5 sheets defined
      45.6% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 13 through 22
      removed outlier: 3.573A  pdb=" N   HIS B  22 " --> pdb=" O   ARG B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 31
    Processing helix  chain 'B' and resid 35 through 42
    Processing helix  chain 'B' and resid 46 through 59
      removed outlier: 3.512A  pdb=" N   GLU B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 74
    Processing helix  chain 'C' and resid 21 through 30
    Processing helix  chain 'C' and resid 35 through 38
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 54 through 66
    Processing helix  chain 'C' and resid 87 through 96
    Processing helix  chain 'C' and resid 105 through 110
    Processing helix  chain 'C' and resid 131 through 143
      removed outlier: 4.323A  pdb=" N   GLN C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 148
      No H-bonds generated for 'chain 'C' and resid 146 through 148'
    Processing helix  chain 'C' and resid 166 through 187
    Processing helix  chain 'C' and resid 190 through 197
    Processing helix  chain 'C' and resid 201 through 206
    Processing helix  chain 'C' and resid 216 through 232
      Proline residue:  C 227  - end of helix
    Processing helix  chain 'C' and resid 246 through 249
      No H-bonds generated for 'chain 'C' and resid 246 through 249'
    Processing helix  chain 'C' and resid 255 through 275
    Processing helix  chain 'C' and resid 304 through 307
    Processing helix  chain 'D' and resid 14 through 22
    Processing helix  chain 'D' and resid 28 through 33
    Processing helix  chain 'D' and resid 36 through 43
    Processing helix  chain 'D' and resid 47 through 61
    Processing helix  chain 'D' and resid 68 through 78
      removed outlier: 3.915A  pdb=" N   THR D  77 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 92
    Processing helix  chain 'D' and resid 113 through 126
    Processing helix  chain 'D' and resid 143 through 153
    Processing helix  chain 'D' and resid 157 through 166
    Processing helix  chain 'D' and resid 175 through 192
    Processing helix  chain 'D' and resid 208 through 213
    Processing helix  chain 'D' and resid 222 through 238
    Processing helix  chain 'D' and resid 265 through 270
      removed outlier: 3.735A  pdb=" N   PHE D 270 " --> pdb=" O   ARG D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 313
      No H-bonds generated for 'chain 'D' and resid 311 through 313'
    Processing helix  chain 'X' and resid 24 through 27
      No H-bonds generated for 'chain 'X' and resid 24 through 27'
    Processing helix  chain 'X' and resid 54 through 66
    Processing helix  chain 'X' and resid 89 through 99
    Processing helix  chain 'X' and resid 105 through 114
      removed outlier: 3.798A  pdb=" N   ARG X 114 " --> pdb=" O   TYR X 110 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 123 through 137
      removed outlier: 4.310A  pdb=" N   SER X 135 " --> pdb=" O   TYR X 131 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET X 136 " --> pdb=" O   SER X 132 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 151 through 161
      removed outlier: 4.333A  pdb=" N   PHE X 154 " --> pdb=" O   LEU X 151 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   TRP X 156 " --> pdb=" O   ALA X 153 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE X 157 " --> pdb=" O   PHE X 154 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASN X 161 " --> pdb=" O   ASP X 158 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 166 through 169
      No H-bonds generated for 'chain 'X' and resid 166 through 169'
    Processing helix  chain 'X' and resid 171 through 186
    Processing helix  chain 'X' and resid 229 through 234
      removed outlier: 4.446A  pdb=" N   LEU X 234 " --> pdb=" O   ALA X 230 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'C' and resid 336 through 339
      removed outlier: 4.150A  pdb=" N   ARG C 322 " --> pdb=" O   PHE C 339 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ARG C 312 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   GLU C 154 " --> pdb=" O   ARG C 237 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL C 239 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL C 156 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   VAL C 241 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE C 158 " --> pdb=" O   VAL C 241 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'C' and resid 340 through 342
    Processing sheet with id=  C, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.539A  pdb=" N   ARG D 275 " --> pdb=" O   ALA D 296 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL D 245 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ILE D 105 " --> pdb=" O   VAL D 245 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   VAL D 247 " --> pdb=" O   ILE D 105 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   GLY D 107 " --> pdb=" O   VAL D 247 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   ASN D 249 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   ASN D 131 " --> pdb=" O   LYS D 201 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   VAL D 203 " --> pdb=" O   ASN D 131 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU D 133 " --> pdb=" O   VAL D 203 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   VAL D 205 " --> pdb=" O   LEU D 133 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL D 135 " --> pdb=" O   VAL D 205 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'D' and resid 251 through 253
    Processing sheet with id=  E, first strand: chain 'X' and resid 276 through 279
      removed outlier: 4.352A  pdb=" N   GLN X 252 " --> pdb=" O   GLN X 244 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   HIS X 237 " --> pdb=" O   ILE X  43 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU X 191 " --> pdb=" O   LEU X  44 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   PHE X  46 " --> pdb=" O   LEU X 191 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ALA X 193 " --> pdb=" O   PHE X  46 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   GLY X  48 " --> pdb=" O   ALA X 193 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   THR X 195 " --> pdb=" O   GLY X  48 " (cutoff:3.500A)

    332 hydrogen bonds defined for protein.
    954 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: 2.00

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2444
        1.34 -     1.46: 1285
        1.46 -     1.57: 3765
        1.57 -     1.69: 25
        1.69 -     1.81: 72
  Bond restraints: 7591
  Sorted by residual:
  bond pdb=" O3A ANP X 301 "
       pdb=" PB  ANP X 301 "
    ideal  model  delta    sigma   weight residual
    1.700  1.553  0.147 2.00e-02 2.50e+03 5.37e+01
  bond pdb=" O3A ANP D 401 "
       pdb=" PB  ANP D 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" O3A ANP C 401 "
       pdb=" PB  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.25e+01
  bond pdb=" N3B ANP X 301 "
       pdb=" PG  ANP X 301 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" N3B ANP C 401 "
       pdb=" PG  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.82e+01
  ... (remaining 7586 not shown)

  Histogram of bond angle deviations from ideal:
       99.71 -   106.57: 213
      106.57 -   113.42: 4305
      113.42 -   120.28: 2740
      120.28 -   127.14: 2946
      127.14 -   134.00: 73
  Bond angle restraints: 10277
  Sorted by residual:
  angle pdb=" PB  ANP X 301 "
        pdb=" N3B ANP X 301 "
        pdb=" PG  ANP X 301 "
      ideal   model   delta    sigma   weight residual
     126.95  109.49   17.46 3.00e+00 1.11e-01 3.39e+01
  angle pdb=" PB  ANP C 401 "
        pdb=" N3B ANP C 401 "
        pdb=" PG  ANP C 401 "
      ideal   model   delta    sigma   weight residual
     126.95  110.36   16.59 3.00e+00 1.11e-01 3.06e+01
  angle pdb=" PB  ANP D 401 "
        pdb=" N3B ANP D 401 "
        pdb=" PG  ANP D 401 "
      ideal   model   delta    sigma   weight residual
     126.95  110.60   16.35 3.00e+00 1.11e-01 2.97e+01
  angle pdb=" C   GLN D 220 "
        pdb=" N   ARG D 221 "
        pdb=" CA  ARG D 221 "
      ideal   model   delta    sigma   weight residual
     122.49  116.55    5.94 1.55e+00 4.16e-01 1.47e+01
  angle pdb=" O1B ANP D 401 "
        pdb=" PB  ANP D 401 "
        pdb=" O2B ANP D 401 "
      ideal   model   delta    sigma   weight residual
     120.08  108.86   11.22 3.00e+00 1.11e-01 1.40e+01
  ... (remaining 10272 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.76: 4232
       19.76 -    39.52: 288
       39.52 -    59.28: 70
       59.28 -    79.04: 31
       79.04 -    98.80: 13
  Dihedral angle restraints: 4634
    sinusoidal: 1963
      harmonic: 2671
  Sorted by residual:
  dihedral pdb=" CA  LEU C 278 "
           pdb=" C   LEU C 278 "
           pdb=" N   ALA C 279 "
           pdb=" CA  ALA C 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.27   17.73     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  THR B  42 "
           pdb=" C   THR B  42 "
           pdb=" N   GLY B  43 "
           pdb=" CA  GLY B  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" O1B ANP C 401 "
           pdb=" N3B ANP C 401 "
           pdb=" PB  ANP C 401 "
           pdb=" PG  ANP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -63.65   98.80     1      3.00e+01 1.11e-03 1.23e+01
  ... (remaining 4631 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 998
       0.057 -    0.113: 187
       0.113 -    0.170: 16
       0.170 -    0.227: 1
       0.227 -    0.283: 3
  Chirality restraints: 1205
  Sorted by residual:
  chirality pdb=" C3' ANP D 401 "
            pdb=" C2' ANP D 401 "
            pdb=" C4' ANP D 401 "
            pdb=" O3' ANP D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C3' ANP X 301 "
            pdb=" C2' ANP X 301 "
            pdb=" C4' ANP X 301 "
            pdb=" O3' ANP X 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" C3' ANP C 401 "
            pdb=" C2' ANP C 401 "
            pdb=" C4' ANP C 401 "
            pdb=" O3' ANP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1202 not shown)

  Planarity restraints: 1267
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 300 "   -0.127 9.50e-02 1.11e+02   5.70e-02 2.04e+00
        pdb=" NE  ARG D 300 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 300 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 300 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 300 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 254 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.89e+00
        pdb=" C   ASP D 254 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ASP D 254 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG D 255 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  46 "   -0.013 2.00e-02 2.50e+03   9.55e-03 1.82e+00
        pdb=" CG  TYR B  46 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  46 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  46 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  46 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  46 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  46 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  46 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1264 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 127
        2.64 -     3.20: 7037
        3.20 -     3.77: 12537
        3.77 -     4.33: 17674
        4.33 -     4.90: 28462
  Nonbonded interactions: 65837
  Sorted by model distance:
  nonbonded pdb=" OG1 THR X  83 "
            pdb=" O   SER X 150 "
     model   vdw
     2.073 2.440
  nonbonded pdb=" O1B ANP D 401 "
            pdb=" O2G ANP D 401 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OG1 THR C 200 "
            pdb=" OD1 ASP C 202 "
     model   vdw
     2.156 2.440
  nonbonded pdb=" O   LEU D  58 "
            pdb=" OG  SER D  62 "
     model   vdw
     2.179 2.440
  nonbonded pdb=" OG  SER B  45 "
            pdb=" O   PRO C  18 "
     model   vdw
     2.192 2.440
  ... (remaining 65832 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.750
  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:          3.980
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     22.950
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
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      :  0.006   0.147   7591  Z= 0.416
  Angle     :  0.818  17.461  10277  Z= 0.372
  Chirality :  0.045   0.283   1205
  Planarity :  0.004   0.057   1267
  Dihedral  : 16.138  98.797   2899
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  0.37 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.15 (0.28), residues: 908
  helix:  0.91 (0.25), residues: 444
  sheet: -0.48 (0.41), residues: 152
  loop : -0.63 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP C 317 
   HIS   0.006   0.001   HIS B  50 
   PHE   0.014   0.001   PHE X  80 
   TYR   0.023   0.002   TYR B  46 
   ARG   0.007   0.001   ARG X 224 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.710 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2217
  time to fit residues: 34.4924
Evaluate side-chains
  104 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1781
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
X 252 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   7591  Z= 0.386
  Angle     :  0.642   9.836  10277  Z= 0.313
  Chirality :  0.045   0.152   1205
  Planarity :  0.005   0.054   1267
  Dihedral  : 11.983  72.246   1146
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.94 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -0.14 (0.28), residues: 908
  helix:  0.65 (0.25), residues: 442
  sheet: -0.77 (0.40), residues: 152
  loop : -0.63 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP C 317 
   HIS   0.005   0.001   HIS D 250 
   PHE   0.012   0.002   PHE X 270 
   TYR   0.012   0.001   TYR B  46 
   ARG   0.006   0.001   ARG X  64 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 120
  average time/residue: 0.2207
  time to fit residues: 35.1766
Evaluate side-chains
  111 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0790
  time to fit residues: 1.8865
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7591  Z= 0.206
  Angle     :  0.505   7.493  10277  Z= 0.254
  Chirality :  0.041   0.169   1205
  Planarity :  0.004   0.034   1267
  Dihedral  : 11.210  72.530   1146
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.93 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.15 (0.28), residues: 908
  helix:  0.99 (0.25), residues: 441
  sheet: -0.71 (0.41), residues: 151
  loop : -0.61 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP C 317 
   HIS   0.003   0.001   HIS D 250 
   PHE   0.010   0.001   PHE D 173 
   TYR   0.008   0.001   TYR B  46 
   ARG   0.004   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.748 
Fit side-chains
  outliers start: 11
  outliers final: 4
  residues processed: 117
  average time/residue: 0.2026
  time to fit residues: 32.0051
Evaluate side-chains
  107 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.745 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0663
  time to fit residues: 1.5396
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
C 276 HIS
D  18 GLN
** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7591  Z= 0.247
  Angle     :  0.528   8.287  10277  Z= 0.263
  Chirality :  0.041   0.168   1205
  Planarity :  0.004   0.035   1267
  Dihedral  : 10.546  72.397   1146
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.53 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.17 (0.28), residues: 908
  helix:  1.04 (0.25), residues: 439
  sheet: -0.78 (0.40), residues: 152
  loop : -0.59 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP C 317 
   HIS   0.003   0.001   HIS C 316 
   PHE   0.011   0.001   PHE X  80 
   TYR   0.007   0.001   TYR C 210 
   ARG   0.004   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.888 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 107
  average time/residue: 0.2253
  time to fit residues: 32.6803
Evaluate side-chains
  103 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.921 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0765
  time to fit residues: 1.8344
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0060
   chunk 78 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
D 131 ASN
** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7591  Z= 0.195
  Angle     :  0.491   6.838  10277  Z= 0.248
  Chirality :  0.040   0.177   1205
  Planarity :  0.003   0.037   1267
  Dihedral  : 10.232  71.877   1146
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.03 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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 (0.28), residues: 908
  helix:  1.18 (0.26), residues: 439
  sheet: -0.70 (0.41), residues: 152
  loop : -0.55 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP C 317 
   HIS   0.003   0.001   HIS X  98 
   PHE   0.012   0.001   PHE X  80 
   TYR   0.008   0.001   TYR B  46 
   ARG   0.004   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.869 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2606
  time to fit residues: 38.9594
Evaluate side-chains
  103 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.874 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1163
  time to fit residues: 2.5453
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 178 GLN
D 138 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7591  Z= 0.192
  Angle     :  0.494   9.752  10277  Z= 0.247
  Chirality :  0.040   0.177   1205
  Planarity :  0.003   0.039   1267
  Dihedral  : 10.082  69.868   1146
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 15.01 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.41 (0.29), residues: 908
  helix:  1.23 (0.26), residues: 439
  sheet: -0.65 (0.41), residues: 152
  loop : -0.48 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP C 317 
   HIS   0.002   0.001   HIS X  98 
   PHE   0.011   0.001   PHE X  80 
   TYR   0.008   0.001   TYR B  46 
   ARG   0.003   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.799 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 103
  average time/residue: 0.2083
  time to fit residues: 29.2816
Evaluate side-chains
  101 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.886 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1339
  time to fit residues: 1.8089
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0050
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0870
   chunk 87 optimal weight:    0.0670
   chunk 54 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.2910

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

Flipped N/Q/H residues before XYZ refinement:
D 138 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7591  Z= 0.144
  Angle     :  0.460   8.686  10277  Z= 0.233
  Chirality :  0.039   0.179   1205
  Planarity :  0.003   0.040   1267
  Dihedral  :  9.935  69.109   1146
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 15.51 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.59 (0.29), residues: 908
  helix:  1.42 (0.26), residues: 438
  sheet: -0.48 (0.41), residues: 154
  loop : -0.49 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP C 317 
   HIS   0.003   0.001   HIS X  86 
   PHE   0.012   0.001   PHE D 173 
   TYR   0.008   0.001   TYR B  46 
   ARG   0.003   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.820 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 110
  average time/residue: 0.2026
  time to fit residues: 30.3729
Evaluate side-chains
  99 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.851 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0733
  time to fit residues: 1.4900
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0370
   chunk 43 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.8460

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

Flipped N/Q/H residues before XYZ refinement:
** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7591  Z= 0.224
  Angle     :  0.514   9.459  10277  Z= 0.255
  Chirality :  0.041   0.164   1205
  Planarity :  0.003   0.039   1267
  Dihedral  : 10.001  70.241   1146
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 15.88 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.50 (0.29), residues: 908
  helix:  1.29 (0.26), residues: 439
  sheet: -0.57 (0.41), residues: 152
  loop : -0.43 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP C 317 
   HIS   0.002   0.001   HIS X  98 
   PHE   0.012   0.001   PHE C  99 
   TYR   0.007   0.001   TYR B  46 
   ARG   0.004   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.825 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 98
  average time/residue: 0.1927
  time to fit residues: 26.4534
Evaluate side-chains
  96 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.866 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0737
  time to fit residues: 1.6388
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    0.0060
   chunk 84 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0970
   chunk 64 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
D 138 ASN
X 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7591  Z= 0.166
  Angle     :  0.473   9.304  10277  Z= 0.239
  Chirality :  0.040   0.194   1205
  Planarity :  0.003   0.039   1267
  Dihedral  :  9.903  72.503   1146
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 16.25 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.59 (0.29), residues: 908
  helix:  1.38 (0.26), residues: 439
  sheet: -0.45 (0.41), residues: 154
  loop : -0.45 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP C 317 
   HIS   0.003   0.001   HIS X  86 
   PHE   0.011   0.001   PHE C  99 
   TYR   0.007   0.001   TYR B  46 
   ARG   0.003   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.875 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 98
  average time/residue: 0.2004
  time to fit residues: 27.1894
Evaluate side-chains
  93 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.821 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0973
  time to fit residues: 1.3266
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0010
   chunk 7 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
D 138 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7591  Z= 0.208
  Angle     :  0.511   9.176  10277  Z= 0.255
  Chirality :  0.041   0.189   1205
  Planarity :  0.003   0.039   1267
  Dihedral  :  9.966  74.413   1146
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 16.75 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.56 (0.29), residues: 908
  helix:  1.33 (0.26), residues: 439
  sheet: -0.51 (0.41), residues: 152
  loop : -0.42 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP C 317 
   HIS   0.002   0.001   HIS X  98 
   PHE   0.012   0.001   PHE C  99 
   TYR   0.007   0.001   TYR B  46 
   ARG   0.003   0.000   ARG D 275 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.884 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 95
  average time/residue: 0.1906
  time to fit residues: 25.4613
Evaluate side-chains
  97 residues out of total 806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.831 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0711
  time to fit residues: 1.5648
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 72 optimal weight:    0.0370
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0670
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
D 138 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.196727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.167928 restraints weight = 8094.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 1.69
r_work: 0.3732 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7591  Z= 0.161
  Angle     :  0.475   8.935  10277  Z= 0.238
  Chirality :  0.039   0.192   1205
  Planarity :  0.003   0.040   1267
  Dihedral  :  9.898  78.105   1146
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 16.87 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.65 (0.29), residues: 908
  helix:  1.44 (0.26), residues: 439
  sheet: -0.41 (0.42), residues: 154
  loop : -0.45 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP C 317 
   HIS   0.003   0.001   HIS X  86 
   PHE   0.012   0.001   PHE D 173 
   TYR   0.007   0.001   TYR B  46 
   ARG   0.003   0.000   ARG D 275 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1890.23 seconds
wall clock time: 35 minutes 13.22 seconds (2113.22 seconds total)