Starting phenix.real_space_refine
on Fri Dec  8 12:20:57 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/12_2023/7xp6_33366_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/12_2023/7xp6_33366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/12_2023/7xp6_33366.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/12_2023/7xp6_33366.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/12_2023/7xp6_33366_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/12_2023/7xp6_33366_updated.pdb"
  }
  resolution = 3.01
  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=   0.023
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      47      5.16       5
     C    5322      2.51       5
     N    1436      2.21       5
     O    1531      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R GLU   70": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8336
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1964
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "G"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 981
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "R"
      Number of atoms: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2330
          Unusual residues: {'SY9': 1}
          Classifications: {'peptide': 283, 'undetermined': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 274, None: 1}
            Not linked:
              pdbres="VAL R 301 "
              pdbres="SY9 R 501 "
          Chain breaks: 1
  Time building chain proxies: 4.82, per 1000 atoms: 0.58
  Number of scatterers: 8336
  At special positions: 0
  Unit cell: (79.04, 101.92, 131.04, 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      47     16.00
     O    1531      8.00
     N    1436      7.00
     C    5322      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 100 " - pdb=" SG  CYS N 108 " distance=2.03

  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: 3.13
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1980

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      41.8% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 35
    Processing helix  chain 'A' and resid 49 through 60
      removed outlier: 3.656A  pdb=" N   LEU A  59 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   HIS A  60 " --> pdb=" O   MET A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 103
    Processing helix  chain 'A' and resid 118 through 132
      removed outlier: 4.184A  pdb=" N   GLN A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   GLU A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 158
    Processing helix  chain 'A' and resid 163 through 166
      No H-bonds generated for 'chain 'A' and resid 163 through 166'
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 187 through 206
    Processing helix  chain 'A' and resid 223 through 246
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 4.578A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 30 through 32
      No H-bonds generated for 'chain 'N' and resid 30 through 32'
    Processing helix  chain 'N' and resid 63 through 65
      No H-bonds generated for 'chain 'N' and resid 63 through 65'
    Processing helix  chain 'N' and resid 89 through 91
      No H-bonds generated for 'chain 'N' and resid 89 through 91'
    Processing helix  chain 'R' and resid 4 through 38
    Processing helix  chain 'R' and resid 43 through 70
    Processing helix  chain 'R' and resid 77 through 110
    Processing helix  chain 'R' and resid 116 through 123
    Processing helix  chain 'R' and resid 125 through 153
      Proline residue:  R 136  - end of helix
    Processing helix  chain 'R' and resid 174 through 212
      removed outlier: 3.568A  pdb=" N   LEU R 182 " --> pdb=" O   THR R 178 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL R 186 " --> pdb=" O   LEU R 182 " (cutoff:3.500A)
      Proline residue:  R 187  - end of helix
      removed outlier: 3.680A  pdb=" N   LEU R 211 " --> pdb=" O   LYS R 207 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   HIS R 212 " --> pdb=" O   LYS R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 253
    Processing helix  chain 'R' and resid 259 through 282
      removed outlier: 3.745A  pdb=" N   PHE R 263 " --> pdb=" O   PRO R 259 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE R 267 " --> pdb=" O   PHE R 263 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA R 268 " --> pdb=" O   CYS R 264 " (cutoff:3.500A)
      Proline residue:  R 272  - end of helix
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 284 through 300
    Processing sheet with id=  A, first strand: chain 'A' and resid 214 through 218
      removed outlier: 7.292A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   HIS A 217 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A 144 " --> pdb=" O   HIS A 217 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 108 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   VAL A  89 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   GLY A  43 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.186A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.678A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.902A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.638A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.450A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.675A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.767A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 4 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 123 through 125
      removed outlier: 6.313A  pdb=" N   ARG N  39 " --> pdb=" O   TRP N  48 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   TRP N  48 " --> pdb=" O   ARG N  39 " (cutoff:3.500A)

    436 hydrogen bonds defined for protein.
    1266 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: 2.40

  Time building geometry restraints manager: 3.44 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: 2696
        1.34 -     1.46: 1999
        1.46 -     1.58: 3757
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 8518
  Sorted by residual:
  bond pdb=" CAV SY9 R 501 "
       pdb=" NAY SY9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.454  1.501 -0.047 2.00e-02 2.50e+03 5.49e+00
  bond pdb=" CAG SY9 R 501 "
       pdb=" CAV SY9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.578  1.544  0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" CAX SY9 R 501 "
       pdb=" NAY SY9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.449  1.482 -0.033 2.00e-02 2.50e+03 2.78e+00
  bond pdb=" N   THR N 112 "
       pdb=" CA  THR N 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.50e+00
  bond pdb=" CAM SY9 R 501 "
       pdb=" OAO SY9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.411  1.434 -0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 8513 not shown)

  Histogram of bond angle deviations from ideal:
       99.67 -   106.54: 180
      106.54 -   113.41: 4709
      113.41 -   120.27: 2954
      120.27 -   127.14: 3612
      127.14 -   134.01: 94
  Bond angle restraints: 11549
  Sorted by residual:
  angle pdb=" CA  PRO R 187 "
        pdb=" N   PRO R 187 "
        pdb=" CD  PRO R 187 "
      ideal   model   delta    sigma   weight residual
     112.00  106.05    5.95 1.40e+00 5.10e-01 1.80e+01
  angle pdb=" C   GLY A 159 "
        pdb=" N   LYS A 160 "
        pdb=" CA  LYS A 160 "
      ideal   model   delta    sigma   weight residual
     121.54  127.94   -6.40 1.91e+00 2.74e-01 1.12e+01
  angle pdb=" CB  MET R 247 "
        pdb=" CG  MET R 247 "
        pdb=" SD  MET R 247 "
      ideal   model   delta    sigma   weight residual
     112.70  122.72  -10.02 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" CA  ARG A 172 "
        pdb=" CB  ARG A 172 "
        pdb=" CG  ARG A 172 "
      ideal   model   delta    sigma   weight residual
     114.10  119.64   -5.54 2.00e+00 2.50e-01 7.66e+00
  angle pdb=" C   ASP B 247 "
        pdb=" N   ALA B 248 "
        pdb=" CA  ALA B 248 "
      ideal   model   delta    sigma   weight residual
     122.74  126.63   -3.89 1.44e+00 4.82e-01 7.29e+00
  ... (remaining 11544 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.38: 5019
       34.38 -    68.76: 74
       68.76 -   103.14: 2
      103.14 -   137.51: 3
      137.51 -   171.89: 1
  Dihedral angle restraints: 5099
    sinusoidal: 2045
      harmonic: 3054
  Sorted by residual:
  dihedral pdb=" CAM SY9 R 501 "
           pdb=" CAP SY9 R 501 "
           pdb=" OAO SY9 R 501 "
           pdb=" CAQ SY9 R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.84   87.05 -171.89     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CAR SY9 R 501 "
           pdb=" CAP SY9 R 501 "
           pdb=" CAQ SY9 R 501 "
           pdb=" OAO SY9 R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.89  -56.55  122.44     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 5096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1073
       0.051 -    0.101: 192
       0.101 -    0.152: 42
       0.152 -    0.203: 3
       0.203 -    0.253: 2
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" NAY SY9 R 501 "
            pdb=" CAS SY9 R 501 "
            pdb=" CAV SY9 R 501 "
            pdb=" CAX SY9 R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.12   -2.38    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CAK SY9 R 501 "
            pdb=" CAG SY9 R 501 "
            pdb=" CAN SY9 R 501 "
            pdb=" NAH SY9 R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.77   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.17 2.00e-01 2.50e+01 6.94e-01
  ... (remaining 1309 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAA SY9 R 501 "    0.233 2.00e-02 2.50e+03   1.59e-01 3.81e+02
        pdb=" CAI SY9 R 501 "   -0.048 2.00e-02 2.50e+03
        pdb=" CAK SY9 R 501 "   -0.105 2.00e-02 2.50e+03
        pdb=" CAL SY9 R 501 "    0.202 2.00e-02 2.50e+03
        pdb=" NAH SY9 R 501 "   -0.189 2.00e-02 2.50e+03
        pdb=" OAJ SY9 R 501 "   -0.093 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 186 "   -0.085 5.00e-02 4.00e+02   1.25e-01 2.51e+01
        pdb=" N   PRO R 187 "    0.217 5.00e-02 4.00e+02
        pdb=" CA  PRO R 187 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO R 187 "   -0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 271 "   -0.047 5.00e-02 4.00e+02   7.18e-02 8.24e+00
        pdb=" N   PRO R 272 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO R 272 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO R 272 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 121
        2.66 -     3.22: 7974
        3.22 -     3.78: 12978
        3.78 -     4.34: 17264
        4.34 -     4.90: 29100
  Nonbonded interactions: 67437
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 173 "
            pdb=" OD2 ASP A 198 "
     model   vdw
     2.100 2.440
  nonbonded pdb=" OG  SER B 275 "
            pdb=" O   SER B 316 "
     model   vdw
     2.183 2.440
  nonbonded pdb=" O   ALA A  44 "
            pdb=" OG  SER A  47 "
     model   vdw
     2.187 2.440
  nonbonded pdb=" OG  SER R 103 "
            pdb=" OG  SER R 194 "
     model   vdw
     2.200 2.440
  nonbonded pdb=" O   TYR A 173 "
            pdb=" NH1 ARG A 191 "
     model   vdw
     2.202 2.520
  ... (remaining 67432 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:             0.850
  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:             0.000
  Extract box with map and model:          3.900
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     25.810
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8518  Z= 0.214
  Angle     :  0.593  10.023  11549  Z= 0.329
  Chirality :  0.042   0.253   1312
  Planarity :  0.007   0.159   1456
  Dihedral  : 13.311 171.893   3113
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.26), residues: 1037
  helix:  2.57 (0.23), residues: 424
  sheet:  0.99 (0.34), residues: 238
  loop : -0.33 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP A  99 
   HIS   0.005   0.001   HIS A 212 
   PHE   0.026   0.001   PHE R   9 
   TYR   0.029   0.002   TYR B  59 
   ARG   0.009   0.000   ARG B 134 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2702
  time to fit residues: 80.5651
Evaluate side-chains
  225 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.915 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3040
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 78 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
B 110 ASN
B 119 ASN
B 155 ASN
R 205 HIS
R 217 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8518  Z= 0.231
  Angle     :  0.527   6.890  11549  Z= 0.286
  Chirality :  0.042   0.197   1312
  Planarity :  0.005   0.072   1456
  Dihedral  :  8.282 152.438   1193
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.34 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.26), residues: 1037
  helix:  2.72 (0.23), residues: 436
  sheet:  0.89 (0.33), residues: 234
  loop : -0.41 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B 169 
   HIS   0.005   0.001   HIS A 212 
   PHE   0.026   0.002   PHE A  87 
   TYR   0.027   0.001   TYR B  59 
   ARG   0.007   0.000   ARG B  46 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 242
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 14
  residues processed: 243
  average time/residue: 0.2725
  time to fit residues: 84.4708
Evaluate side-chains
  237 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 223
  time to evaluate  : 0.885 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.1386
  time to fit residues: 4.2192
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A 126 ASN
B  16 ASN
B 119 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 217 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8518  Z= 0.227
  Angle     :  0.517   8.457  11549  Z= 0.276
  Chirality :  0.041   0.186   1312
  Planarity :  0.004   0.064   1456
  Dihedral  :  7.829 143.509   1193
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 13.63 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.26), residues: 1037
  helix:  2.70 (0.23), residues: 437
  sheet:  0.69 (0.34), residues: 232
  loop : -0.37 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B 169 
   HIS   0.005   0.001   HIS A 212 
   PHE   0.025   0.001   PHE A  87 
   TYR   0.023   0.001   TYR B  59 
   ARG   0.004   0.000   ARG A  38 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 242
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 6
  residues processed: 244
  average time/residue: 0.2667
  time to fit residues: 83.2381
Evaluate side-chains
  243 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 237
  time to evaluate  : 0.975 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0864
  time to fit residues: 2.2946
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0970
   chunk 94 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 126 ASN
B  88 ASN
B 119 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  14 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8518  Z= 0.187
  Angle     :  0.504  10.828  11549  Z= 0.262
  Chirality :  0.040   0.145   1312
  Planarity :  0.004   0.061   1456
  Dihedral  :  6.473 126.006   1193
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.07 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.26), residues: 1037
  helix:  2.79 (0.23), residues: 437
  sheet:  0.75 (0.33), residues: 232
  loop : -0.41 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B 169 
   HIS   0.004   0.001   HIS A 212 
   PHE   0.027   0.001   PHE A  87 
   TYR   0.018   0.001   TYR B  59 
   ARG   0.004   0.000   ARG A  38 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 237
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 9
  residues processed: 242
  average time/residue: 0.2962
  time to fit residues: 91.8974
Evaluate side-chains
  233 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 224
  time to evaluate  : 0.864 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1390
  time to fit residues: 3.2076
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 74 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8518  Z= 0.292
  Angle     :  0.536   8.523  11549  Z= 0.284
  Chirality :  0.042   0.224   1312
  Planarity :  0.004   0.057   1456
  Dihedral  :  4.335  20.676   1193
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.09 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.37 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.60 (0.26), residues: 1037
  helix:  2.59 (0.24), residues: 437
  sheet:  0.49 (0.33), residues: 231
  loop : -0.41 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.002   TRP R  66 
   HIS   0.005   0.001   HIS A  85 
   PHE   0.031   0.002   PHE A  87 
   TYR   0.020   0.002   TYR B  59 
   ARG   0.004   0.000   ARG A  38 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 254
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 13
  residues processed: 262
  average time/residue: 0.2580
  time to fit residues: 87.0749
Evaluate side-chains
  258 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 245
  time to evaluate  : 0.903 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0824
  time to fit residues: 3.2181
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 134 ASN
B 119 ASN
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  14 GLN
R  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8518  Z= 0.253
  Angle     :  0.529   6.529  11549  Z= 0.281
  Chirality :  0.041   0.164   1312
  Planarity :  0.004   0.053   1456
  Dihedral  :  4.265  21.753   1193
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.80 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 18.24 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.56 (0.26), residues: 1037
  helix:  2.54 (0.24), residues: 437
  sheet:  0.43 (0.33), residues: 235
  loop : -0.39 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.025   0.002   TRP R  66 
   HIS   0.004   0.001   HIS A  85 
   PHE   0.030   0.002   PHE A  87 
   TYR   0.017   0.001   TYR B  59 
   ARG   0.003   0.000   ARG A  38 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 250
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 252
  average time/residue: 0.2585
  time to fit residues: 83.8353
Evaluate side-chains
  258 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 250
  time to evaluate  : 0.923 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1361
  time to fit residues: 2.9541
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 119 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 ASN
** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8518  Z= 0.223
  Angle     :  0.523  10.255  11549  Z= 0.275
  Chirality :  0.041   0.180   1312
  Planarity :  0.004   0.050   1456
  Dihedral  :  4.188  22.155   1193
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.80 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 17.91 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1037
  helix:  2.59 (0.24), residues: 437
  sheet:  0.35 (0.33), residues: 236
  loop : -0.33 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP R  97 
   HIS   0.005   0.001   HIS A  85 
   PHE   0.029   0.001   PHE A  87 
   TYR   0.015   0.001   TYR B  59 
   ARG   0.004   0.000   ARG A 211 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 241
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 243
  average time/residue: 0.2672
  time to fit residues: 83.2955
Evaluate side-chains
  245 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 240
  time to evaluate  : 0.893 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0843
  time to fit residues: 2.0056
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A 134 ASN
B 119 ASN
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 ASN
** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8518  Z= 0.275
  Angle     :  0.549   8.560  11549  Z= 0.293
  Chirality :  0.042   0.175   1312
  Planarity :  0.004   0.049   1456
  Dihedral  :  4.280  23.731   1193
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.99 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 19.34 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1037
  helix:  2.46 (0.24), residues: 437
  sheet:  0.35 (0.33), residues: 230
  loop : -0.40 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP R  97 
   HIS   0.006   0.001   HIS A  85 
   PHE   0.030   0.002   PHE A  87 
   TYR   0.017   0.001   TYR B  59 
   ARG   0.008   0.000   ARG A 211 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 252
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 252
  average time/residue: 0.2667
  time to fit residues: 85.8104
Evaluate side-chains
  255 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 247
  time to evaluate  : 0.919 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1390
  time to fit residues: 2.9390
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 95 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A 226 ASN
B 119 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 ASN
** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8518  Z= 0.252
  Angle     :  0.556   7.979  11549  Z= 0.295
  Chirality :  0.042   0.164   1312
  Planarity :  0.004   0.053   1456
  Dihedral  :  4.238  24.163   1193
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 20.00 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1037
  helix:  2.39 (0.24), residues: 437
  sheet:  0.37 (0.33), residues: 229
  loop : -0.43 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP R  97 
   HIS   0.006   0.001   HIS A  85 
   PHE   0.032   0.002   PHE A  87 
   TYR   0.015   0.001   TYR B  59 
   ARG   0.007   0.000   ARG A 211 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 230
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 232
  average time/residue: 0.2774
  time to fit residues: 81.9282
Evaluate side-chains
  228 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 0.986 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0866
  time to fit residues: 1.8869
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0670
   chunk 81 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
B 119 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 ASN
R 224 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8518  Z= 0.217
  Angle     :  0.562   9.783  11549  Z= 0.296
  Chirality :  0.042   0.162   1312
  Planarity :  0.004   0.063   1456
  Dihedral  :  4.206  24.379   1193
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.99 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1037
  helix:  2.48 (0.24), residues: 431
  sheet:  0.35 (0.33), residues: 229
  loop : -0.40 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP R  97 
   HIS   0.007   0.001   HIS A  85 
   PHE   0.032   0.001   PHE A  87 
   TYR   0.015   0.001   TYR B  59 
   ARG   0.007   0.000   ARG A 211 

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2898
  time to fit residues: 82.3386
Evaluate side-chains
  224 residues out of total 910 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.922 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3112
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0000
   chunk 71 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 ASN
B 155 ASN
R  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.138341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.120092 restraints weight = 12762.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.34
r_work: 0.3496 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8518  Z= 0.244
  Angle     :  0.571  10.011  11549  Z= 0.301
  Chirality :  0.042   0.159   1312
  Planarity :  0.004   0.062   1456
  Dihedral  :  4.212  22.670   1193
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 21.21 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1037
  helix:  2.41 (0.24), residues: 430
  sheet:  0.43 (0.33), residues: 227
  loop : -0.39 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP R  97 
   HIS   0.005   0.001   HIS A 212 
   PHE   0.030   0.002   PHE A  87 
   TYR   0.018   0.001   TYR B  59 
   ARG   0.007   0.000   ARG A 211 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2338.97 seconds
wall clock time: 43 minutes 7.33 seconds (2587.33 seconds total)