Starting phenix.real_space_refine
on Mon Mar 11 06:33:02 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/03_2024/7bz2_30249_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/03_2024/7bz2_30249.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/03_2024/7bz2_30249.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/03_2024/7bz2_30249.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/03_2024/7bz2_30249_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/03_2024/7bz2_30249_updated.pdb"
  }
  resolution = 3.82
  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=   0.005
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      44      5.16       5
     C    4725      2.51       5
     N    1275      2.21       5
     O    1349      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   11": "OD1" <-> "OD2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A PHE  208": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  273": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  314": "OE1" <-> "OE2"
    Residue "A PHE  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  378": "OD1" <-> "OD2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "B ASP   66": "OD1" <-> "OD2"
    Residue "B ASP  153": "OD1" <-> "OD2"
    Residue "B ASP  170": "OD1" <-> "OD2"
    Residue "B ASP  195": "OD1" <-> "OD2"
    Residue "B ASP  205": "OD1" <-> "OD2"
    Residue "B ASP  212": "OD1" <-> "OD2"
    Residue "B PHE  234": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  291": "OD1" <-> "OD2"
    Residue "N PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU   46": "OE1" <-> "OE2"
    Residue "N ARG   98": "NH1" <-> "NH2"
    Residue "R GLU   30": "OE1" <-> "OE2"
    Residue "R PHE   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  223": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  225": "OE1" <-> "OE2"
    Residue "R GLU  268": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7393
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1561
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 3, 'TRANS': 194}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLU:plan': 4, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 81
    Chain: "B"
      Number of atoms: 2453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2453
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "G"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 246
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "N"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 956
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2177
          Unusual residues: {'H98': 1}
          Classifications: {'peptide': 285, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 7, 'TRANS': 277, None: 1}
            Not linked:
              pdbres="LEU R 340 "
              pdbres="H98 R 401 "
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 197
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 102
  Time building chain proxies: 4.39, per 1000 atoms: 0.59
  Number of scatterers: 7393
  At special positions: 0
  Unit cell: (92.22, 96.46, 117.66, 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      44     16.00
     O    1349      8.00
     N    1275      7.00
     C    4725      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 2.94
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      29.8% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 13
      No H-bonds generated for 'chain 'A' and resid 11 through 13'
    Processing helix  chain 'A' and resid 15 through 37
      removed outlier: 3.705A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LYS A  28 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
      removed outlier: 3.641A  pdb=" N   SER A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 4.822A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 388
      removed outlier: 3.959A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ILE A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 24
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 16 through 23
    Processing helix  chain 'G' and resid 30 through 44
      removed outlier: 4.199A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS G  41 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 59
      removed outlier: 3.822A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL R  52 " --> pdb=" O   VAL R  48 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ALA R  57 " --> pdb=" O   LEU R  53 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 84
      removed outlier: 4.070A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR R  73 " --> pdb=" O   ASN R  69 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA R  78 " --> pdb=" O   SER R  74 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASP R  79 " --> pdb=" O   LEU R  75 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   MET R  82 " --> pdb=" O   ALA R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 96
      removed outlier: 3.579A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ILE R  94 " --> pdb=" O   GLY R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 136
      removed outlier: 3.671A  pdb=" N   VAL R 114 " --> pdb=" O   THR R 110 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU R 115 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR R 118 " --> pdb=" O   VAL R 114 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 141
      No H-bonds generated for 'chain 'R' and resid 138 through 141'
    Processing helix  chain 'R' and resid 152 through 160
      removed outlier: 4.246A  pdb=" N   ILE R 159 " --> pdb=" O   LEU R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 165
      No H-bonds generated for 'chain 'R' and resid 162 through 165'
    Processing helix  chain 'R' and resid 167 through 170
      No H-bonds generated for 'chain 'R' and resid 167 through 170'
    Processing helix  chain 'R' and resid 181 through 183
      No H-bonds generated for 'chain 'R' and resid 181 through 183'
    Processing helix  chain 'R' and resid 199 through 202
      No H-bonds generated for 'chain 'R' and resid 199 through 202'
    Processing helix  chain 'R' and resid 204 through 207
      No H-bonds generated for 'chain 'R' and resid 204 through 207'
    Processing helix  chain 'R' and resid 210 through 226
      removed outlier: 4.139A  pdb=" N   TYR R 219 " --> pdb=" O   MET R 215 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLU R 225 " --> pdb=" O   ARG R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 273 through 298
      removed outlier: 4.915A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.764A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 308
      No H-bonds generated for 'chain 'R' and resid 305 through 308'
    Processing helix  chain 'R' and resid 311 through 314
      No H-bonds generated for 'chain 'R' and resid 311 through 314'
    Processing helix  chain 'R' and resid 322 through 324
      No H-bonds generated for 'chain 'R' and resid 322 through 324'
    Processing helix  chain 'R' and resid 330 through 335
    Processing sheet with id=  A, first strand: chain 'A' and resid 40 through 42
      removed outlier: 6.679A  pdb=" N   ASN A 218 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.765A  pdb=" N   LEU A  46 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 288 through 291
      removed outlier: 6.166A  pdb=" N   TYR A 360 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A 291 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   HIS A 362 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'B' and resid 78 through 82
      removed outlier: 3.984A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 284 through 286
    Processing sheet with id=  F, first strand: chain 'B' and resid 250 through 253
      removed outlier: 3.715A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=  H, first strand: chain 'N' and resid 10 through 13
      removed outlier: 3.682A  pdb=" N   VAL N  12 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASN N  35 " --> pdb=" O   ALA N  97 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 17 through 20
      removed outlier: 3.512A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)

    179 hydrogen bonds defined for protein.
    519 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2395
        1.34 -     1.46: 1787
        1.46 -     1.58: 3294
        1.58 -     1.70: 0
        1.70 -     1.81: 62
  Bond restraints: 7538
  Sorted by residual:
  bond pdb=" C19 H98 R 401 "
       pdb=" N2  H98 R 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.391 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C3  H98 R 401 "
       pdb=" C4  H98 R 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.480  0.023 2.00e-02 2.50e+03 1.31e+00
  bond pdb=" C13 H98 R 401 "
       pdb=" C14 H98 R 401 "
    ideal  model  delta    sigma   weight residual
    1.392  1.370  0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" CA  GLY A  47 "
       pdb=" C   GLY A  47 "
    ideal  model  delta    sigma   weight residual
    1.514  1.499  0.015 1.41e-02 5.03e+03 1.19e+00
  bond pdb=" CB  TRP B  82 "
       pdb=" CG  TRP B  82 "
    ideal  model  delta    sigma   weight residual
    1.498  1.465  0.033 3.10e-02 1.04e+03 1.13e+00
  ... (remaining 7533 not shown)

  Histogram of bond angle deviations from ideal:
       99.65 -   106.53: 140
      106.53 -   113.41: 4134
      113.41 -   120.28: 2827
      120.28 -   127.16: 3065
      127.16 -   134.04: 79
  Bond angle restraints: 10245
  Sorted by residual:
  angle pdb=" N   VAL R  31 "
        pdb=" CA  VAL R  31 "
        pdb=" C   VAL R  31 "
      ideal   model   delta    sigma   weight residual
     113.53  109.98    3.55 9.80e-01 1.04e+00 1.31e+01
  angle pdb=" C   GLU B 172 "
        pdb=" N   THR B 173 "
        pdb=" CA  THR B 173 "
      ideal   model   delta    sigma   weight residual
     121.54  128.13   -6.59 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" C15 H98 R 401 "
        pdb=" N2  H98 R 401 "
        pdb=" C19 H98 R 401 "
      ideal   model   delta    sigma   weight residual
     129.13  120.75    8.38 3.00e+00 1.11e-01 7.80e+00
  angle pdb=" N   GLY B 162 "
        pdb=" CA  GLY B 162 "
        pdb=" C   GLY B 162 "
      ideal   model   delta    sigma   weight residual
     113.18  107.08    6.10 2.37e+00 1.78e-01 6.62e+00
  angle pdb=" CA  LEU A 393 "
        pdb=" CB  LEU A 393 "
        pdb=" CG  LEU A 393 "
      ideal   model   delta    sigma   weight residual
     116.30  124.44   -8.14 3.50e+00 8.16e-02 5.40e+00
  ... (remaining 10240 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3942
       17.95 -    35.90: 383
       35.90 -    53.85: 64
       53.85 -    71.81: 17
       71.81 -    89.76: 6
  Dihedral angle restraints: 4412
    sinusoidal: 1573
      harmonic: 2839
  Sorted by residual:
  dihedral pdb=" CA  PHE R 290 "
           pdb=" C   PHE R 290 "
           pdb=" N   ILE R 291 "
           pdb=" CA  ILE R 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.15   25.85     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -47.65  -38.35     1      1.00e+01 1.00e-02 2.07e+01
  dihedral pdb=" CA  ASN R  69 "
           pdb=" C   ASN R  69 "
           pdb=" N   TYR R  70 "
           pdb=" CA  TYR R  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 4409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 627
       0.030 -    0.060: 364
       0.060 -    0.091: 128
       0.091 -    0.121: 64
       0.121 -    0.151: 11
  Chirality restraints: 1194
  Sorted by residual:
  chirality pdb=" CG  LEU A 291 "
            pdb=" CB  LEU A 291 "
            pdb=" CD1 LEU A 291 "
            pdb=" CD2 LEU A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  TYR R 219 "
            pdb=" N   TYR R 219 "
            pdb=" C   TYR R 219 "
            pdb=" CB  TYR R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 1191 not shown)

  Planarity restraints: 1295
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO R 168 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.032 5.00e-02 4.00e+02   4.86e-02 3.79e+00
        pdb=" N   PRO B 236 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "    0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO N  88 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1292 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 146
        2.66 -     3.22: 7141
        3.22 -     3.78: 10523
        3.78 -     4.34: 14194
        4.34 -     4.90: 23778
  Nonbonded interactions: 55782
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.101 2.440
  nonbonded pdb=" OD2 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.134 2.440
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.193 2.440
  nonbonded pdb=" OD1 ASP B 291 "
            pdb=" ND2 ASN B 293 "
     model   vdw
     2.204 2.520
  nonbonded pdb=" OG  SER R 203 "
            pdb=" O2  H98 R 401 "
     model   vdw
     2.221 2.440
  ... (remaining 55777 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 group one per residue
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:             0.270
  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:          1.700
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     23.670
  Find NCS groups from input model:        0.220
  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:             0.010
  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:   28.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7538  Z= 0.275
  Angle     :  0.680   8.376  10245  Z= 0.376
  Chirality :  0.046   0.151   1194
  Planarity :  0.004   0.050   1295
  Dihedral  : 15.119  89.757   2564
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  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: -6.04 (0.20), residues: 950
  helix: -3.35 (0.21), residues: 342
  sheet: -4.69 (0.26), residues: 190
  loop : -4.15 (0.21), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 109 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.014   0.002   PHE N 108 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.003   0.000   ARG N 118 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: B  111 TYR cc_start: 0.7918 (m-80) cc_final: 0.7697 (m-80)
REVERT: R  227 LYS cc_start: 0.8479 (ttpt) cc_final: 0.7850 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2124
  time to fit residues: 51.5062
Evaluate side-chains
  144 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0040
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0980
   chunk 74 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 213 GLN
A 371 ASN
B 176 GLN
B 230 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
N  39 GLN
R 142 GLN
R 148 ASN
R 312 ASN
R 322 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7538  Z= 0.156
  Angle     :  0.568   7.735  10245  Z= 0.297
  Chirality :  0.043   0.138   1194
  Planarity :  0.003   0.047   1295
  Dihedral  :  7.393  82.033   1058
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.71 %
    Favored  : 79.43 %
  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: -4.98 (0.22), residues: 950
  helix: -2.35 (0.25), residues: 354
  sheet: -4.34 (0.28), residues: 189
  loop : -3.55 (0.24), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 313 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.032   0.001   PHE R 208 
 TYR   0.013   0.001   TYR G  40 
 ARG   0.005   0.000   ARG R 239 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8348 (tt)
REVERT: B  228 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8170 (p0)
REVERT: N   12 VAL cc_start: 0.7963 (t) cc_final: 0.7755 (t)
REVERT: N   83 MET cc_start: 0.7239 (mtp) cc_final: 0.7020 (mtp)
  outliers start: 21
  outliers final: 12
  residues processed: 176
  average time/residue: 0.1754
  time to fit residues: 42.2393
Evaluate side-chains
  160 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 86 optimal weight:    0.1980
   chunk 93 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B  75 GLN
B 176 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 148 ASN
R 293 ASN
R 312 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7538  Z= 0.142
  Angle     :  0.540   8.311  10245  Z= 0.279
  Chirality :  0.042   0.139   1194
  Planarity :  0.003   0.046   1295
  Dihedral  :  6.885  84.635   1058
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.89 %
    Favored  : 76.43 %
  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: -4.35 (0.24), residues: 950
  helix: -1.94 (0.26), residues: 355
  sheet: -3.90 (0.30), residues: 194
  loop : -3.09 (0.26), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.017   0.001   PHE A 222 
 TYR   0.013   0.001   TYR B 111 
 ARG   0.004   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8410 (tt)
REVERT: B  111 TYR cc_start: 0.7712 (m-80) cc_final: 0.7273 (m-80)
REVERT: B  154 ASP cc_start: 0.7923 (m-30) cc_final: 0.7373 (t0)
REVERT: B  228 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8006 (p0)
REVERT: R  312 ASN cc_start: 0.6792 (OUTLIER) cc_final: 0.6444 (t0)
  outliers start: 27
  outliers final: 15
  residues processed: 166
  average time/residue: 0.1540
  time to fit residues: 36.1494
Evaluate side-chains
  155 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0370
   chunk 45 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0010
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5064

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 175 GLN
B 183 HIS
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7538  Z= 0.133
  Angle     :  0.526   7.448  10245  Z= 0.273
  Chirality :  0.042   0.130   1194
  Planarity :  0.003   0.044   1295
  Dihedral  :  6.590  85.406   1058
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 20.30 %
    Favored  : 75.34 %
  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: -3.90 (0.25), residues: 950
  helix: -1.57 (0.27), residues: 354
  sheet: -3.65 (0.31), residues: 198
  loop : -2.83 (0.27), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.014   0.001   PHE R 193 
 TYR   0.008   0.001   TYR B 111 
 ARG   0.004   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8403 (tt)
REVERT: B   75 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7353 (mp-120)
REVERT: B  101 MET cc_start: 0.8880 (mmm) cc_final: 0.8523 (mtt)
REVERT: B  228 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7984 (p0)
REVERT: R   64 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6869 (mt)
REVERT: R  312 ASN cc_start: 0.6624 (OUTLIER) cc_final: 0.6183 (t0)
  outliers start: 32
  outliers final: 20
  residues processed: 157
  average time/residue: 0.1675
  time to fit residues: 36.7924
Evaluate side-chains
  152 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 52 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 82 optimal weight:   30.0000
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B  75 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN
R 142 GLN
R 312 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7538  Z= 0.268
  Angle     :  0.605   9.673  10245  Z= 0.314
  Chirality :  0.044   0.145   1194
  Planarity :  0.004   0.044   1295
  Dihedral  :  6.995  89.842   1058
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 23.02 %
    Favored  : 72.48 %
  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: -3.93 (0.25), residues: 950
  helix: -1.62 (0.27), residues: 356
  sheet: -3.52 (0.31), residues: 214
  loop : -2.84 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 109 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.016   0.002   PHE A 222 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.005   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8673 (tt)
REVERT: A  289 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7945 (mp)
REVERT: B  154 ASP cc_start: 0.7917 (m-30) cc_final: 0.7393 (t0)
REVERT: B  228 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7775 (p0)
REVERT: R  235 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7406 (ttpt)
REVERT: R  312 ASN cc_start: 0.6567 (OUTLIER) cc_final: 0.6076 (t0)
  outliers start: 33
  outliers final: 22
  residues processed: 162
  average time/residue: 0.1675
  time to fit residues: 37.7327
Evaluate side-chains
  157 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 82 optimal weight:   30.0000
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 91 optimal weight:    0.0980
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 7 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0970
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 176 GLN
B 183 HIS
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7538  Z= 0.128
  Angle     :  0.533   7.544  10245  Z= 0.272
  Chirality :  0.042   0.141   1194
  Planarity :  0.003   0.043   1295
  Dihedral  :  6.324  82.585   1058
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.25 %
    Favored  : 72.07 %
  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: -3.42 (0.26), residues: 950
  helix: -1.22 (0.28), residues: 356
  sheet: -3.40 (0.31), residues: 199
  loop : -2.49 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.009   0.001   TYR A 360 
 ARG   0.005   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8442 (tt)
REVERT: A  212 PHE cc_start: 0.7215 (p90) cc_final: 0.6937 (p90)
REVERT: B  154 ASP cc_start: 0.7908 (m-30) cc_final: 0.7292 (t0)
REVERT: B  228 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8036 (p0)
REVERT: G   38 MET cc_start: 0.6681 (ttp) cc_final: 0.6235 (tpt)
REVERT: N   60 TYR cc_start: 0.8723 (m-80) cc_final: 0.8379 (m-80)
REVERT: R   36 MET cc_start: 0.7127 (mmt) cc_final: 0.6684 (mmm)
REVERT: R   64 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6973 (mt)
REVERT: R  235 LYS cc_start: 0.7462 (ttmt) cc_final: 0.7248 (ttpt)
REVERT: R  300 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.6964 (m-30)
REVERT: R  312 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.6008 (t0)
  outliers start: 27
  outliers final: 18
  residues processed: 154
  average time/residue: 0.1656
  time to fit residues: 35.7936
Evaluate side-chains
  150 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 67 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   7538  Z= 0.311
  Angle     :  0.621   9.879  10245  Z= 0.323
  Chirality :  0.045   0.230   1194
  Planarity :  0.004   0.043   1295
  Dihedral  :  6.843  85.105   1058
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 25.61 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.26), residues: 950
  helix: -1.42 (0.28), residues: 356
  sheet: -3.35 (0.31), residues: 216
  loop : -2.63 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 109 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.015   0.002   PHE A 222 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.009   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: B  101 MET cc_start: 0.8947 (mmm) cc_final: 0.8668 (mtt)
REVERT: B  154 ASP cc_start: 0.7892 (m-30) cc_final: 0.7397 (t0)
REVERT: B  228 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7732 (p0)
REVERT: R  196 ASN cc_start: 0.7687 (p0) cc_final: 0.7477 (p0)
REVERT: R  304 ARG cc_start: 0.6545 (ttp-110) cc_final: 0.6016 (mtm-85)
REVERT: R  312 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.6249 (t0)
  outliers start: 31
  outliers final: 22
  residues processed: 156
  average time/residue: 0.1692
  time to fit residues: 36.8013
Evaluate side-chains
  158 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0870
   chunk 87 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B 156 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7538  Z= 0.158
  Angle     :  0.556   8.610  10245  Z= 0.282
  Chirality :  0.042   0.160   1194
  Planarity :  0.003   0.043   1295
  Dihedral  :  6.408  83.369   1058
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 26.70 %
    Favored  : 69.21 %
  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: -3.28 (0.26), residues: 950
  helix: -1.17 (0.28), residues: 357
  sheet: -3.24 (0.32), residues: 202
  loop : -2.37 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE A 222 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.006   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8666 (tt)
REVERT: A  212 PHE cc_start: 0.7321 (p90) cc_final: 0.7018 (p90)
REVERT: B  154 ASP cc_start: 0.7942 (m-30) cc_final: 0.7358 (t0)
REVERT: B  228 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7562 (p0)
REVERT: G   38 MET cc_start: 0.6741 (ttp) cc_final: 0.6278 (tpt)
REVERT: R   64 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7116 (mt)
REVERT: R  312 ASN cc_start: 0.6394 (OUTLIER) cc_final: 0.6064 (t0)
  outliers start: 30
  outliers final: 16
  residues processed: 149
  average time/residue: 0.1726
  time to fit residues: 35.7369
Evaluate side-chains
  142 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0670
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 90 optimal weight:    0.5980
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7538  Z= 0.145
  Angle     :  0.555   8.294  10245  Z= 0.279
  Chirality :  0.042   0.160   1194
  Planarity :  0.003   0.051   1295
  Dihedral  :  6.205  84.652   1058
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 26.43 %
    Favored  : 69.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.05 (0.26), residues: 950
  helix: -0.98 (0.28), residues: 357
  sheet: -3.01 (0.33), residues: 199
  loop : -2.33 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 289 
 TYR   0.007   0.001   TYR B  59 
 ARG   0.014   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8660 (tt)
REVERT: A  212 PHE cc_start: 0.7274 (p90) cc_final: 0.7020 (p90)
REVERT: B  154 ASP cc_start: 0.7955 (m-30) cc_final: 0.7347 (t0)
REVERT: B  228 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8152 (p0)
REVERT: G   38 MET cc_start: 0.6711 (ttp) cc_final: 0.6258 (tpt)
REVERT: N   60 TYR cc_start: 0.8671 (m-80) cc_final: 0.8323 (m-80)
REVERT: R   64 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7027 (mt)
REVERT: R  312 ASN cc_start: 0.6441 (OUTLIER) cc_final: 0.6147 (t0)
  outliers start: 28
  outliers final: 20
  residues processed: 144
  average time/residue: 0.1671
  time to fit residues: 33.6407
Evaluate side-chains
  144 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0980
   chunk 94 optimal weight:    0.0030
   chunk 87 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0470
   chunk 59 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.3088

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7538  Z= 0.127
  Angle     :  0.543   8.194  10245  Z= 0.273
  Chirality :  0.041   0.163   1194
  Planarity :  0.003   0.051   1295
  Dihedral  :  5.998  85.341   1058
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 27.11 %
    Favored  : 69.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.80 (0.27), residues: 950
  helix: -0.70 (0.29), residues: 355
  sheet: -2.88 (0.33), residues: 198
  loop : -2.26 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.013   0.001   PHE N 103 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.012   0.000   ARG R 304 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8615 (tt)
REVERT: A  212 PHE cc_start: 0.7301 (p90) cc_final: 0.7066 (p90)
REVERT: B  154 ASP cc_start: 0.7985 (m-30) cc_final: 0.7324 (t0)
REVERT: G   38 MET cc_start: 0.6666 (ttp) cc_final: 0.6243 (tpt)
REVERT: N   60 TYR cc_start: 0.8657 (m-80) cc_final: 0.8320 (m-80)
REVERT: R   64 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7005 (mt)
REVERT: R  300 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6986 (m-30)
  outliers start: 23
  outliers final: 15
  residues processed: 138
  average time/residue: 0.1719
  time to fit residues: 32.9938
Evaluate side-chains
  136 residues out of total 842 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Chi-restraints excluded: chain R residue  311 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0020
   chunk 66 optimal weight:    4.9990
   chunk 4 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.175605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146056 restraints weight = 8142.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142584 restraints weight = 12583.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144803 restraints weight = 11574.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7538  Z= 0.147
  Angle     :  0.544   8.070  10245  Z= 0.273
  Chirality :  0.042   0.168   1194
  Planarity :  0.003   0.048   1295
  Dihedral  :  5.988  88.577   1058
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 27.38 %
    Favored  : 69.62 %
  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: -2.65 (0.27), residues: 950
  helix: -0.51 (0.30), residues: 347
  sheet: -2.85 (0.33), residues: 198
  loop : -2.19 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.013   0.001   PHE N 103 
 TYR   0.007   0.001   TYR B  59 
 ARG   0.011   0.000   ARG R 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1664.53 seconds
wall clock time: 30 minutes 51.67 seconds (1851.67 seconds total)