Starting phenix.real_space_refine
on Fri Jul 25 15:35:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0s_23102/07_2025/7l0s_23102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0s_23102/07_2025/7l0s_23102.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l0s_23102/07_2025/7l0s_23102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0s_23102/07_2025/7l0s_23102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0s_23102/07_2025/7l0s_23102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0s_23102/07_2025/7l0s_23102.cif"
  }
  resolution = 4.5
  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=   0.002
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      57      5.16       5
     C    5034      2.51       5
     N    1343      2.21       5
     O    1472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7906
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 2424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2424
          Classifications: {'peptide': 308}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 297}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 2729
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 337, 2694
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 4, 'TRANS': 332}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 337, 2694
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 4, 'TRANS': 332}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 2697
    Chain: "B"
      Number of atoms: 2385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2385
          Classifications: {'peptide': 311}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 305}
    Chain: "G"
      Number of atoms: 310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 310
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 3, 'TRANS': 35}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AASP A  97 " occ=0.56
      ... (14 atoms not shown)
      pdb=" OD2BASP A  97 " occ=0.44
    residue:
      pdb=" N  AARG A 105 " occ=0.68
      ... (20 atoms not shown)
      pdb=" NH2BARG A 105 " occ=0.32
    residue:
      pdb=" N  AASP A 158 " occ=0.51
      ... (14 atoms not shown)
      pdb=" OD2BASP A 158 " occ=0.49
    residue:
      pdb=" N  AASP A 160 " occ=0.44
      ... (14 atoms not shown)
      pdb=" OD2BASP A 160 " occ=0.56
  Time building chain proxies: 6.65, per 1000 atoms: 0.84
  Number of scatterers: 7906
  At special positions: 0
  Unit cell: (88.275, 117.15, 121.275, 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      57     16.00
     O    1472      8.00
     N    1343      7.00
     C    5034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 225 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.04
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      48.2% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'C' and resid 60 through 91
    Processing helix  chain 'C' and resid 100 through 129
      Proline residue:  C 122  - end of helix
    Processing helix  chain 'C' and resid 137 through 173
    Processing helix  chain 'C' and resid 173 through 181
    Processing helix  chain 'C' and resid 182 through 202
    Processing helix  chain 'C' and resid 202 through 207
      removed outlier: 3.519A  pdb=" N   THR C 207 " --> pdb=" O   PRO C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 270
      Proline residue:  C 249  - end of helix
    Processing helix  chain 'C' and resid 300 through 334
      Proline residue:  C 323  - end of helix
      removed outlier: 3.533A  pdb=" N   ILE C 334 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 371
      Proline residue:  C 366  - end of helix
    Processing helix  chain 'C' and resid 373 through 385
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.507A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 65 through 68
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.598A  pdb=" N   GLY A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 114
      removed outlier: 3.851A  pdb=" N   ASP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 133
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.541A  pdb=" N  AASP A 158 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.781A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.404A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'G' and resid 32 through 48
    Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190
      removed outlier: 6.527A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.895A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.837A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.974A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.399A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.062A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.903A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1234 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: 2.42

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1635
        1.33 -     1.45: 1967
        1.45 -     1.57: 4376
        1.57 -     1.69: 2
        1.69 -     1.82: 83
  Bond restraints: 8063
  Sorted by residual:
  bond pdb=" C   HIS C 133 "
       pdb=" N   PRO C 134 "
    ideal  model  delta    sigma   weight residual
    1.331  1.385 -0.054 1.28e-02 6.10e+03 1.76e+01
  bond pdb=" N   LEU B  95 "
       pdb=" CA  LEU B  95 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.17e-02 7.31e+03 7.73e+00
  bond pdb=" CA  ILE A  81 "
       pdb=" CB  ILE A  81 "
    ideal  model  delta    sigma   weight residual
    1.540  1.572 -0.032 1.29e-02 6.01e+03 6.26e+00
  bond pdb=" N   ASP A 309 "
       pdb=" CA  ASP A 309 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.33e-02 5.65e+03 6.23e+00
  bond pdb=" N   LEU C 256 "
       pdb=" CA  LEU C 256 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.17e-02 7.31e+03 6.21e+00
  ... (remaining 8058 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 10074
        2.30 -     4.60: 709
        4.60 -     6.90: 96
        6.90 -     9.20: 37
        9.20 -    11.50: 10
  Bond angle restraints: 10926
  Sorted by residual:
  angle pdb=" N   PHE C 376 "
        pdb=" CA  PHE C 376 "
        pdb=" C   PHE C 376 "
      ideal   model   delta    sigma   weight residual
     112.54  105.52    7.02 1.22e+00 6.72e-01 3.31e+01
  angle pdb=" N   VAL C 131 "
        pdb=" CA  VAL C 131 "
        pdb=" C   VAL C 131 "
      ideal   model   delta    sigma   weight residual
     107.51   99.04    8.47 1.49e+00 4.50e-01 3.23e+01
  angle pdb=" N   LYS A  46 "
        pdb=" CA  LYS A  46 "
        pdb=" C   LYS A  46 "
      ideal   model   delta    sigma   weight residual
     111.28  105.15    6.13 1.09e+00 8.42e-01 3.16e+01
  angle pdb=" N   GLY B 141 "
        pdb=" CA  GLY B 141 "
        pdb=" C   GLY B 141 "
      ideal   model   delta    sigma   weight residual
     113.18  101.68   11.50 2.37e+00 1.78e-01 2.35e+01
  angle pdb=" C   SER B 227 "
        pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
      ideal   model   delta    sigma   weight residual
     120.82  127.94   -7.12 1.47e+00 4.63e-01 2.35e+01
  ... (remaining 10921 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 4300
       15.98 -    31.97: 369
       31.97 -    47.95: 86
       47.95 -    63.93: 30
       63.93 -    79.91: 4
  Dihedral angle restraints: 4789
    sinusoidal: 1862
      harmonic: 2927
  Sorted by residual:
  dihedral pdb=" CB  CYS C 142 "
           pdb=" SG  CYS C 142 "
           pdb=" SG  CYS C 225 "
           pdb=" CB  CYS C 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.91   79.91     1      1.00e+01 1.00e-02 7.92e+01
  dihedral pdb=" CA  PHE G  64 "
           pdb=" C   PHE G  64 "
           pdb=" N   LYS G  65 "
           pdb=" CA  LYS G  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.93   26.07     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  ASP B 290 "
           pdb=" C   ASP B 290 "
           pdb=" N   ASP B 291 "
           pdb=" CA  ASP B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.28   23.72     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 4786 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 932
       0.082 -    0.164: 261
       0.164 -    0.246: 45
       0.246 -    0.328: 13
       0.328 -    0.410: 1
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  HIS C 133 "
            pdb=" N   HIS C 133 "
            pdb=" C   HIS C 133 "
            pdb=" CB  HIS C 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CB  VAL C 266 "
            pdb=" CA  VAL C 266 "
            pdb=" CG1 VAL C 266 "
            pdb=" CG2 VAL C 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.19e+00
  ... (remaining 1249 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 374 "    0.027 2.00e-02 2.50e+03   5.29e-02 2.80e+01
        pdb=" C   ALA C 374 "   -0.091 2.00e-02 2.50e+03
        pdb=" O   ALA C 374 "    0.034 2.00e-02 2.50e+03
        pdb=" N   ASN C 375 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  49 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   ARG B  49 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ARG B  49 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR B  50 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 191 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   SER B 191 "    0.055 2.00e-02 2.50e+03
        pdb=" O   SER B 191 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 192 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 221
        2.67 -     3.22: 7554
        3.22 -     3.78: 13158
        3.78 -     4.34: 16982
        4.34 -     4.90: 27714
  Nonbonded interactions: 65629
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 146 "
            pdb=" OXT LEU D  13 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" NZ  LYS A 128 "
            pdb=" OD1AASP A 160 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" N   GLU A  43 "
            pdb=" OE1 GLU A  43 "
     model   vdw
     2.286 3.120
  ... (remaining 65624 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.32 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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.750
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
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      :  0.008   0.081   8064  Z= 0.425
  Angle     :  1.345  11.500  10928  Z= 0.786
  Chirality :  0.079   0.410   1252
  Planarity :  0.008   0.061   1384
  Dihedral  : 13.518  70.452   2896
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.80 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.21 %
  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: -3.19 (0.22), residues: 992
  helix: -1.81 (0.19), residues: 461
  sheet: -2.25 (0.36), residues: 173
  loop : -2.15 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.004   TRP B 297 
 HIS   0.008   0.003   HIS B  54 
 PHE   0.038   0.004   PHE C 376 
 TYR   0.029   0.004   TYR C 349 
 ARG   0.013   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13720 (  423)
  hydrogen bonds       : angle       7.40797 ( 1234)
  SS BOND              : bond        0.00329 (    1)
  SS BOND              : angle       1.87474 (    2)
  covalent geometry    : bond        0.00800 ( 8063)
  covalent geometry    : angle       1.34494 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 316
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7195 (pp)
REVERT: C   87 PHE cc_start: 0.5700 (t80) cc_final: 0.5394 (m-10)
REVERT: C  105 TYR cc_start: 0.7591 (m-80) cc_final: 0.7375 (m-80)
REVERT: C  153 THR cc_start: 0.7532 (m) cc_final: 0.7254 (m)
REVERT: C  169 LEU cc_start: 0.8763 (tp) cc_final: 0.8547 (tp)
REVERT: C  242 THR cc_start: 0.8417 (t) cc_final: 0.8115 (t)
REVERT: C  325 HIS cc_start: 0.7032 (m-70) cc_final: 0.5956 (m-70)
REVERT: C  376 PHE cc_start: 0.5539 (t80) cc_final: 0.4751 (t80)
REVERT: A   28 GLU cc_start: 0.8284 (tt0) cc_final: 0.7792 (tm-30)
REVERT: B   79 LEU cc_start: 0.9083 (pt) cc_final: 0.8600 (pp)
REVERT: B  149 CYS cc_start: 0.7744 (p) cc_final: 0.7450 (m)
REVERT: B  233 CYS cc_start: 0.7340 (p) cc_final: 0.7044 (p)
REVERT: B  275 SER cc_start: 0.9186 (t) cc_final: 0.8629 (m)
REVERT: B  276 VAL cc_start: 0.8726 (m) cc_final: 0.8477 (m)
REVERT: B  329 THR cc_start: 0.8680 (t) cc_final: 0.8475 (t)
REVERT: B  337 LYS cc_start: 0.8774 (mttm) cc_final: 0.8372 (mptt)
REVERT: G   32 LEU cc_start: 0.8607 (tp) cc_final: 0.8281 (tp)
REVERT: G   37 CYS cc_start: 0.7880 (p) cc_final: 0.6775 (p)
REVERT: G   46 GLU cc_start: 0.8395 (tt0) cc_final: 0.7607 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 322
  average time/residue: 0.2244
  time to fit residues: 92.7967
Evaluate side-chains
  216 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 212
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN
C 132 HIS
C 159 ASN
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 262 ASN
C 292 ASN
A  79 GLN
A 172 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
B  75 GLN
B  88 ASN
B 142 HIS
B 230 ASN
B 259 GLN
B 295 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.107232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.077359 restraints weight = 94755.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.082755 restraints weight = 36479.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.085392 restraints weight = 19361.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8064  Z= 0.258
  Angle     :  0.792   9.759  10928  Z= 0.426
  Chirality :  0.047   0.169   1252
  Planarity :  0.005   0.046   1384
  Dihedral  :  5.704  61.534   1092
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  4.65 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.25), residues: 992
  helix: -0.34 (0.22), residues: 463
  sheet: -1.86 (0.36), residues: 177
  loop : -1.47 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 339 
 HIS   0.007   0.002   HIS B 266 
 PHE   0.025   0.003   PHE A 199 
 TYR   0.026   0.002   TYR B 264 
 ARG   0.006   0.001   ARG G  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05258 (  423)
  hydrogen bonds       : angle       5.61239 ( 1234)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       1.06298 (    2)
  covalent geometry    : bond        0.00532 ( 8063)
  covalent geometry    : angle       0.79217 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 235
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: C  168 TYR cc_start: 0.7409 (t80) cc_final: 0.6904 (t80)
REVERT: C  169 LEU cc_start: 0.8754 (tp) cc_final: 0.8323 (tp)
REVERT: C  246 PHE cc_start: 0.8007 (t80) cc_final: 0.7803 (t80)
REVERT: C  267 MET cc_start: 0.8633 (mtm) cc_final: 0.8294 (mtp)
REVERT: C  325 HIS cc_start: 0.8332 (m-70) cc_final: 0.8123 (m-70)
REVERT: C  330 MET cc_start: 0.7822 (tpp) cc_final: 0.7280 (ttp)
REVERT: C  350 PHE cc_start: 0.8706 (t80) cc_final: 0.8497 (t80)
REVERT: A   18 MET cc_start: 0.8360 (tmm) cc_final: 0.8151 (tmm)
REVERT: A   32 ARG cc_start: 0.8150 (tpm170) cc_final: 0.7938 (tpm170)
REVERT: A  209 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8647 (ttpp)
REVERT: A  259 PHE cc_start: 0.8810 (m-80) cc_final: 0.8599 (m-80)
REVERT: B   57 LYS cc_start: 0.8901 (mttt) cc_final: 0.8676 (mtmt)
REVERT: B  146 LEU cc_start: 0.9108 (mp) cc_final: 0.8732 (mt)
REVERT: B  149 CYS cc_start: 0.7896 (p) cc_final: 0.7634 (m)
REVERT: B  213 VAL cc_start: 0.7825 (t) cc_final: 0.7078 (p)
REVERT: B  233 CYS cc_start: 0.7975 (p) cc_final: 0.7657 (p)
REVERT: B  246 ASP cc_start: 0.8344 (m-30) cc_final: 0.7918 (m-30)
REVERT: B  337 LYS cc_start: 0.9094 (mttm) cc_final: 0.8703 (mptt)
REVERT: G   34 SER cc_start: 0.8766 (m) cc_final: 0.8449 (m)
REVERT: G   37 CYS cc_start: 0.8524 (p) cc_final: 0.7835 (p)
REVERT: G   38 GLU cc_start: 0.8949 (mp0) cc_final: 0.8586 (mm-30)
REVERT: G   41 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8444 (ttp80)
REVERT: G   42 ASP cc_start: 0.8187 (p0) cc_final: 0.7951 (p0)
  outliers start: 4
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2178
  time to fit residues: 69.3721
Evaluate side-chains
  174 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.107895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.078091 restraints weight = 94071.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.082632 restraints weight = 33521.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.085794 restraints weight = 17493.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8064  Z= 0.186
  Angle     :  0.712   7.792  10928  Z= 0.383
  Chirality :  0.045   0.251   1252
  Planarity :  0.004   0.047   1384
  Dihedral  :  5.321  55.982   1092
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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: -1.00 (0.26), residues: 992
  helix:  0.21 (0.23), residues: 465
  sheet: -1.35 (0.39), residues: 171
  loop : -1.32 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.025   0.002   PHE A 108 
 TYR   0.024   0.002   TYR B 124 
 ARG   0.005   0.001   ARG C 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04706 (  423)
  hydrogen bonds       : angle       5.36206 ( 1234)
  SS BOND              : bond        0.01349 (    1)
  SS BOND              : angle       1.55485 (    2)
  covalent geometry    : bond        0.00388 ( 8063)
  covalent geometry    : angle       0.71182 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 TYR cc_start: 0.7204 (m-80) cc_final: 0.6996 (m-80)
REVERT: C  121 MET cc_start: 0.8355 (tpt) cc_final: 0.7679 (tpt)
REVERT: C  166 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8472 (tm-30)
REVERT: C  168 TYR cc_start: 0.7600 (t80) cc_final: 0.7358 (t80)
REVERT: C  267 MET cc_start: 0.8639 (mtm) cc_final: 0.8269 (mtm)
REVERT: C  321 TRP cc_start: 0.9067 (m100) cc_final: 0.8572 (m100)
REVERT: C  330 MET cc_start: 0.7779 (tpp) cc_final: 0.7107 (ttp)
REVERT: C  352 MET cc_start: 0.8568 (mmt) cc_final: 0.8107 (mmp)
REVERT: C  359 TYR cc_start: 0.7368 (m-10) cc_final: 0.6749 (m-80)
REVERT: D   11 TYR cc_start: 0.7691 (p90) cc_final: 0.7424 (p90)
REVERT: A   18 MET cc_start: 0.8328 (tmm) cc_final: 0.8064 (tmm)
REVERT: A   32 ARG cc_start: 0.8026 (tpm170) cc_final: 0.7684 (tpm170)
REVERT: A  194 LEU cc_start: 0.8599 (tt) cc_final: 0.8381 (mp)
REVERT: A  209 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8633 (ttpp)
REVERT: A  259 PHE cc_start: 0.8893 (m-80) cc_final: 0.8610 (m-80)
REVERT: A  265 ILE cc_start: 0.9115 (mt) cc_final: 0.8792 (mm)
REVERT: B   57 LYS cc_start: 0.8945 (mttt) cc_final: 0.8610 (mtmt)
REVERT: B   61 MET cc_start: 0.7977 (ppp) cc_final: 0.7741 (ppp)
REVERT: B   75 GLN cc_start: 0.8719 (mm110) cc_final: 0.8466 (mm110)
REVERT: B  146 LEU cc_start: 0.8867 (mp) cc_final: 0.8652 (mp)
REVERT: B  246 ASP cc_start: 0.8462 (m-30) cc_final: 0.7903 (m-30)
REVERT: G   37 CYS cc_start: 0.8321 (p) cc_final: 0.7869 (p)
REVERT: G   38 GLU cc_start: 0.8877 (mp0) cc_final: 0.8505 (mm-30)
REVERT: G   41 ARG cc_start: 0.8769 (pmt-80) cc_final: 0.7851 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2288
  time to fit residues: 72.8250
Evaluate side-chains
  166 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
C 262 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.110055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.083760 restraints weight = 113711.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.087985 restraints weight = 48166.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.090701 restraints weight = 23577.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.5052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8064  Z= 0.147
  Angle     :  0.647   8.397  10928  Z= 0.350
  Chirality :  0.044   0.196   1252
  Planarity :  0.004   0.048   1384
  Dihedral  :  4.988  48.435   1092
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.27), residues: 992
  helix:  0.79 (0.24), residues: 458
  sheet: -0.75 (0.39), residues: 180
  loop : -1.33 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE A 199 
 TYR   0.021   0.002   TYR B 124 
 ARG   0.005   0.000   ARG C 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  423)
  hydrogen bonds       : angle       5.06403 ( 1234)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.38806 (    2)
  covalent geometry    : bond        0.00309 ( 8063)
  covalent geometry    : angle       0.64720 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: C  168 TYR cc_start: 0.7532 (t80) cc_final: 0.7247 (t80)
REVERT: C  224 VAL cc_start: 0.6428 (m) cc_final: 0.6214 (m)
REVERT: C  267 MET cc_start: 0.8617 (mtm) cc_final: 0.8291 (mtm)
REVERT: C  321 TRP cc_start: 0.8992 (m100) cc_final: 0.8487 (m100)
REVERT: C  330 MET cc_start: 0.7541 (tpp) cc_final: 0.6990 (ttp)
REVERT: C  359 TYR cc_start: 0.7147 (m-10) cc_final: 0.6712 (m-80)
REVERT: A   20 ASP cc_start: 0.9287 (m-30) cc_final: 0.8961 (m-30)
REVERT: A   32 ARG cc_start: 0.7753 (tpm170) cc_final: 0.7439 (tpm170)
REVERT: A   37 LEU cc_start: 0.8364 (tp) cc_final: 0.8145 (tt)
REVERT: A  194 LEU cc_start: 0.8887 (tt) cc_final: 0.8371 (mp)
REVERT: A  209 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8627 (ttpp)
REVERT: A  259 PHE cc_start: 0.8665 (m-80) cc_final: 0.8328 (m-80)
REVERT: B   57 LYS cc_start: 0.8906 (mttt) cc_final: 0.8522 (mtmt)
REVERT: B  146 LEU cc_start: 0.8877 (mp) cc_final: 0.8572 (mp)
REVERT: B  210 LEU cc_start: 0.9380 (tt) cc_final: 0.9054 (tt)
REVERT: B  246 ASP cc_start: 0.8613 (m-30) cc_final: 0.8004 (m-30)
REVERT: B  308 LEU cc_start: 0.9219 (tp) cc_final: 0.8968 (tp)
REVERT: B  337 LYS cc_start: 0.8904 (mptt) cc_final: 0.8625 (mptt)
REVERT: G   37 CYS cc_start: 0.8129 (p) cc_final: 0.7653 (p)
REVERT: G   38 GLU cc_start: 0.8893 (mp0) cc_final: 0.8452 (mm-30)
REVERT: G   41 ARG cc_start: 0.8788 (pmt-80) cc_final: 0.8021 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2659
  time to fit residues: 87.1790
Evaluate side-chains
  168 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0980
   chunk 78 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 106 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.108226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.082301 restraints weight = 94108.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.084831 restraints weight = 35880.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.087584 restraints weight = 20276.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.5437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8064  Z= 0.180
  Angle     :  0.702   7.561  10928  Z= 0.373
  Chirality :  0.046   0.243   1252
  Planarity :  0.004   0.049   1384
  Dihedral  :  5.080  41.271   1092
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  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: -0.33 (0.27), residues: 992
  helix:  0.83 (0.24), residues: 458
  sheet: -0.64 (0.41), residues: 168
  loop : -1.29 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.032   0.002   PHE A 108 
 TYR   0.026   0.002   TYR B  59 
 ARG   0.018   0.001   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  423)
  hydrogen bonds       : angle       5.20403 ( 1234)
  SS BOND              : bond        0.00942 (    1)
  SS BOND              : angle       2.54268 (    2)
  covalent geometry    : bond        0.00383 ( 8063)
  covalent geometry    : angle       0.70163 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8336 (tm-30)
REVERT: C  267 MET cc_start: 0.8679 (mtm) cc_final: 0.8306 (mtp)
REVERT: C  321 TRP cc_start: 0.9047 (m100) cc_final: 0.8556 (m100)
REVERT: C  330 MET cc_start: 0.7428 (tpp) cc_final: 0.6909 (ttp)
REVERT: C  352 MET cc_start: 0.8645 (mmt) cc_final: 0.8232 (mmt)
REVERT: C  359 TYR cc_start: 0.7125 (m-80) cc_final: 0.6891 (m-80)
REVERT: A   25 GLU cc_start: 0.8683 (pt0) cc_final: 0.8442 (mm-30)
REVERT: A   32 ARG cc_start: 0.7899 (tpm170) cc_final: 0.7554 (tpm170)
REVERT: A  194 LEU cc_start: 0.8660 (tt) cc_final: 0.8390 (mp)
REVERT: A  209 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8637 (ttpp)
REVERT: A  259 PHE cc_start: 0.8873 (m-80) cc_final: 0.8356 (m-80)
REVERT: B   57 LYS cc_start: 0.8739 (mttt) cc_final: 0.8379 (mtmt)
REVERT: B   61 MET cc_start: 0.7844 (ppp) cc_final: 0.7614 (ppp)
REVERT: B  146 LEU cc_start: 0.8771 (mp) cc_final: 0.8486 (mp)
REVERT: B  246 ASP cc_start: 0.8684 (m-30) cc_final: 0.8042 (m-30)
REVERT: B  311 HIS cc_start: 0.7986 (m-70) cc_final: 0.7539 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1782
  time to fit residues: 53.2276
Evaluate side-chains
  162 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 ASN
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.110223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.085482 restraints weight = 95398.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.088094 restraints weight = 35237.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.089908 restraints weight = 20634.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3409
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8064  Z= 0.135
  Angle     :  0.670   7.684  10928  Z= 0.355
  Chirality :  0.044   0.234   1252
  Planarity :  0.004   0.055   1384
  Dihedral  :  4.799  31.530   1092
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.27), residues: 992
  helix:  0.99 (0.24), residues: 458
  sheet: -0.19 (0.41), residues: 172
  loop : -1.29 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.031   0.001   PHE A 108 
 TYR   0.016   0.001   TYR B 124 
 ARG   0.004   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  423)
  hydrogen bonds       : angle       5.00440 ( 1234)
  SS BOND              : bond        0.00078 (    1)
  SS BOND              : angle       1.25562 (    2)
  covalent geometry    : bond        0.00284 ( 8063)
  covalent geometry    : angle       0.66989 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8295 (tm-30)
REVERT: C  267 MET cc_start: 0.8616 (mtm) cc_final: 0.8252 (mtp)
REVERT: C  301 GLN cc_start: 0.8034 (pm20) cc_final: 0.7188 (tt0)
REVERT: C  321 TRP cc_start: 0.9024 (m100) cc_final: 0.8627 (m100)
REVERT: C  330 MET cc_start: 0.7403 (tpp) cc_final: 0.7095 (ttp)
REVERT: C  352 MET cc_start: 0.8654 (mmt) cc_final: 0.8206 (mmp)
REVERT: D   12 ILE cc_start: 0.8192 (mp) cc_final: 0.7967 (mt)
REVERT: A   25 GLU cc_start: 0.8692 (pt0) cc_final: 0.8433 (mm-30)
REVERT: A   32 ARG cc_start: 0.7648 (tpm170) cc_final: 0.7373 (tpm170)
REVERT: A  194 LEU cc_start: 0.8730 (tt) cc_final: 0.8218 (mp)
REVERT: A  209 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8600 (ttpp)
REVERT: A  251 ASP cc_start: 0.8249 (t0) cc_final: 0.7868 (t0)
REVERT: A  259 PHE cc_start: 0.8861 (m-80) cc_final: 0.8320 (m-80)
REVERT: A  265 ILE cc_start: 0.9052 (mt) cc_final: 0.8746 (mm)
REVERT: A  277 LYS cc_start: 0.7402 (tttt) cc_final: 0.7006 (tttt)
REVERT: B   61 MET cc_start: 0.7974 (ppp) cc_final: 0.7740 (ppp)
REVERT: B  246 ASP cc_start: 0.8858 (m-30) cc_final: 0.8137 (m-30)
REVERT: B  311 HIS cc_start: 0.7761 (m-70) cc_final: 0.7399 (m-70)
REVERT: G   31 MET cc_start: 0.3619 (ptt) cc_final: 0.3103 (ptp)
REVERT: G   38 GLU cc_start: 0.8930 (mp0) cc_final: 0.8518 (mm-30)
REVERT: G   41 ARG cc_start: 0.8813 (pmt-80) cc_final: 0.7906 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1699
  time to fit residues: 51.7732
Evaluate side-chains
  163 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  22 ASN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 ASN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.107993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.080439 restraints weight = 105616.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.085717 restraints weight = 42082.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.086935 restraints weight = 20310.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.6042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8064  Z= 0.178
  Angle     :  0.699   7.882  10928  Z= 0.371
  Chirality :  0.046   0.289   1252
  Planarity :  0.004   0.071   1384
  Dihedral  :  4.918  25.683   1092
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.28), residues: 992
  helix:  0.98 (0.24), residues: 455
  sheet: -0.16 (0.41), residues: 180
  loop : -1.27 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP B 339 
 HIS   0.010   0.002   HIS B 225 
 PHE   0.029   0.002   PHE A 108 
 TYR   0.020   0.002   TYR B  59 
 ARG   0.006   0.001   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04385 (  423)
  hydrogen bonds       : angle       5.11643 ( 1234)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       1.31839 (    2)
  covalent geometry    : bond        0.00379 ( 8063)
  covalent geometry    : angle       0.69846 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: C  244 MET cc_start: 0.8582 (ppp) cc_final: 0.8352 (ppp)
REVERT: C  246 PHE cc_start: 0.7588 (t80) cc_final: 0.7383 (t80)
REVERT: C  267 MET cc_start: 0.8725 (mtm) cc_final: 0.8360 (mtp)
REVERT: C  293 MET cc_start: 0.6402 (pmm) cc_final: 0.5452 (ppp)
REVERT: C  321 TRP cc_start: 0.8999 (m100) cc_final: 0.8624 (m100)
REVERT: C  330 MET cc_start: 0.7413 (tpp) cc_final: 0.6937 (ttm)
REVERT: C  348 HIS cc_start: 0.8068 (m90) cc_final: 0.7728 (m90)
REVERT: C  352 MET cc_start: 0.8561 (mmt) cc_final: 0.8094 (mmp)
REVERT: C  359 TYR cc_start: 0.7496 (m-10) cc_final: 0.7158 (m-80)
REVERT: D   12 ILE cc_start: 0.8241 (mp) cc_final: 0.8035 (mt)
REVERT: A   25 GLU cc_start: 0.8679 (pt0) cc_final: 0.8427 (mm-30)
REVERT: A   32 ARG cc_start: 0.7570 (tpm170) cc_final: 0.7334 (tpm170)
REVERT: A  155 TYR cc_start: 0.8534 (m-80) cc_final: 0.7976 (m-80)
REVERT: A  194 LEU cc_start: 0.8553 (tt) cc_final: 0.8220 (mp)
REVERT: A  209 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8683 (ttpt)
REVERT: A  248 LYS cc_start: 0.8364 (ptpp) cc_final: 0.7976 (pttm)
REVERT: A  259 PHE cc_start: 0.8812 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  265 ILE cc_start: 0.9055 (mt) cc_final: 0.8630 (mm)
REVERT: A  277 LYS cc_start: 0.7336 (tttt) cc_final: 0.6995 (tttt)
REVERT: A  297 GLU cc_start: 0.8388 (pm20) cc_final: 0.8064 (pm20)
REVERT: A  347 ASN cc_start: 0.8765 (m-40) cc_final: 0.8506 (m110)
REVERT: B   61 MET cc_start: 0.7689 (ppp) cc_final: 0.7469 (ppp)
REVERT: B  246 ASP cc_start: 0.8680 (m-30) cc_final: 0.7985 (m-30)
REVERT: G   31 MET cc_start: 0.3392 (ptt) cc_final: 0.2932 (mpp)
REVERT: G   38 GLU cc_start: 0.8990 (mp0) cc_final: 0.8400 (mp0)
REVERT: G   44 VAL cc_start: 0.9174 (m) cc_final: 0.8824 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1982
  time to fit residues: 56.5518
Evaluate side-chains
  161 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:   30.0000
   chunk 75 optimal weight:    2.9990
   chunk 84 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN
C 257 ASN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.110055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.083465 restraints weight = 93988.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.087685 restraints weight = 34450.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.088788 restraints weight = 19666.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.6210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8064  Z= 0.143
  Angle     :  0.679   8.164  10928  Z= 0.358
  Chirality :  0.044   0.196   1252
  Planarity :  0.004   0.049   1384
  Dihedral  :  4.770  20.552   1092
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  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:  0.04 (0.28), residues: 992
  helix:  1.04 (0.24), residues: 458
  sheet:  0.05 (0.42), residues: 171
  loop : -1.25 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.028   0.001   PHE A 108 
 TYR   0.015   0.001   TYR A 287 
 ARG   0.002   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  423)
  hydrogen bonds       : angle       5.03985 ( 1234)
  SS BOND              : bond        0.00547 (    1)
  SS BOND              : angle       1.32127 (    2)
  covalent geometry    : bond        0.00302 ( 8063)
  covalent geometry    : angle       0.67850 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.8007 (tpt) cc_final: 0.7765 (tpt)
REVERT: C  166 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: C  204 MET cc_start: 0.5333 (ppp) cc_final: 0.4047 (mmt)
REVERT: C  267 MET cc_start: 0.8671 (mtm) cc_final: 0.8368 (mtp)
REVERT: C  293 MET cc_start: 0.6227 (pmm) cc_final: 0.5143 (ppp)
REVERT: C  301 GLN cc_start: 0.8053 (pm20) cc_final: 0.7245 (tt0)
REVERT: C  321 TRP cc_start: 0.8959 (m100) cc_final: 0.8597 (m100)
REVERT: C  330 MET cc_start: 0.7399 (tpp) cc_final: 0.6939 (ttp)
REVERT: C  348 HIS cc_start: 0.8213 (m90) cc_final: 0.7844 (m90)
REVERT: C  352 MET cc_start: 0.8703 (mmt) cc_final: 0.8295 (mmp)
REVERT: C  359 TYR cc_start: 0.7463 (m-10) cc_final: 0.6976 (m-10)
REVERT: D   12 ILE cc_start: 0.8195 (mp) cc_final: 0.7815 (mt)
REVERT: A   25 GLU cc_start: 0.8708 (pt0) cc_final: 0.8379 (mm-30)
REVERT: A   32 ARG cc_start: 0.7538 (tpm170) cc_final: 0.7337 (tpm170)
REVERT: A  155 TYR cc_start: 0.8660 (m-80) cc_final: 0.8104 (m-80)
REVERT: A  194 LEU cc_start: 0.8477 (tt) cc_final: 0.8164 (mp)
REVERT: A  248 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7918 (pttm)
REVERT: A  251 ASP cc_start: 0.8082 (t0) cc_final: 0.7722 (t0)
REVERT: A  259 PHE cc_start: 0.8834 (m-80) cc_final: 0.8291 (m-80)
REVERT: A  265 ILE cc_start: 0.9079 (mt) cc_final: 0.8758 (mm)
REVERT: A  277 LYS cc_start: 0.7338 (tttt) cc_final: 0.7058 (tttt)
REVERT: A  297 GLU cc_start: 0.8428 (pm20) cc_final: 0.8189 (pm20)
REVERT: A  347 ASN cc_start: 0.8795 (m-40) cc_final: 0.8539 (m110)
REVERT: B  246 ASP cc_start: 0.8784 (m-30) cc_final: 0.7937 (m-30)
REVERT: B  275 SER cc_start: 0.8730 (t) cc_final: 0.8439 (m)
REVERT: B  311 HIS cc_start: 0.7627 (m-70) cc_final: 0.7324 (m-70)
REVERT: G   31 MET cc_start: 0.3285 (ptt) cc_final: 0.2944 (mpp)
REVERT: G   41 ARG cc_start: 0.8847 (pmt-80) cc_final: 0.7731 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.2027
  time to fit residues: 58.9086
Evaluate side-chains
  163 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0770
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.112402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.084927 restraints weight = 89718.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.089534 restraints weight = 33590.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.093566 restraints weight = 16485.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.6388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8064  Z= 0.134
  Angle     :  0.688   8.426  10928  Z= 0.358
  Chirality :  0.044   0.176   1252
  Planarity :  0.004   0.053   1384
  Dihedral  :  4.645  18.786   1092
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.27), residues: 992
  helix:  1.10 (0.24), residues: 458
  sheet: -0.06 (0.42), residues: 167
  loop : -1.11 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.028   0.002   PHE A 108 
 TYR   0.012   0.001   TYR C 369 
 ARG   0.006   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04165 (  423)
  hydrogen bonds       : angle       5.07254 ( 1234)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       1.28776 (    2)
  covalent geometry    : bond        0.00283 ( 8063)
  covalent geometry    : angle       0.68817 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  204 MET cc_start: 0.5091 (ppp) cc_final: 0.3952 (mmt)
REVERT: C  293 MET cc_start: 0.5982 (pmm) cc_final: 0.4965 (ppp)
REVERT: C  301 GLN cc_start: 0.7955 (pm20) cc_final: 0.7183 (tt0)
REVERT: C  321 TRP cc_start: 0.8897 (m100) cc_final: 0.8675 (m100)
REVERT: C  330 MET cc_start: 0.7316 (tpp) cc_final: 0.6941 (ttp)
REVERT: C  348 HIS cc_start: 0.8187 (m90) cc_final: 0.7881 (m90)
REVERT: C  352 MET cc_start: 0.8740 (mmt) cc_final: 0.8337 (mmp)
REVERT: C  359 TYR cc_start: 0.7505 (m-10) cc_final: 0.6763 (m-10)
REVERT: D   12 ILE cc_start: 0.8002 (mp) cc_final: 0.7582 (mt)
REVERT: A   25 GLU cc_start: 0.8676 (pt0) cc_final: 0.8367 (mm-30)
REVERT: A  155 TYR cc_start: 0.8693 (m-80) cc_final: 0.8128 (m-80)
REVERT: A  248 LYS cc_start: 0.8209 (ptpp) cc_final: 0.7802 (pttm)
REVERT: A  251 ASP cc_start: 0.7920 (t0) cc_final: 0.7602 (t0)
REVERT: A  259 PHE cc_start: 0.8816 (m-80) cc_final: 0.8271 (m-80)
REVERT: A  265 ILE cc_start: 0.9131 (mt) cc_final: 0.8825 (mm)
REVERT: A  277 LYS cc_start: 0.7343 (tttt) cc_final: 0.7098 (tttt)
REVERT: A  297 GLU cc_start: 0.8332 (pm20) cc_final: 0.8105 (pm20)
REVERT: B  275 SER cc_start: 0.8557 (t) cc_final: 0.8338 (m)
REVERT: B  311 HIS cc_start: 0.7704 (m-70) cc_final: 0.7402 (m-70)
REVERT: G   38 GLU cc_start: 0.8902 (mp0) cc_final: 0.7958 (mp0)
REVERT: G   41 ARG cc_start: 0.8794 (pmt-80) cc_final: 0.7174 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.2520
  time to fit residues: 74.4911
Evaluate side-chains
  154 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 21 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:
C 257 ASN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.112497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.084976 restraints weight = 112483.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.089762 restraints weight = 40860.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.091689 restraints weight = 20556.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.6592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8064  Z= 0.142
  Angle     :  0.709   8.396  10928  Z= 0.371
  Chirality :  0.045   0.188   1252
  Planarity :  0.004   0.057   1384
  Dihedral  :  4.683  20.319   1092
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.27), residues: 992
  helix:  1.14 (0.24), residues: 455
  sheet: -0.13 (0.40), residues: 167
  loop : -1.19 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.028   0.002   PHE A 108 
 TYR   0.023   0.001   TYR C 359 
 ARG   0.008   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04264 (  423)
  hydrogen bonds       : angle       5.10658 ( 1234)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       1.37468 (    2)
  covalent geometry    : bond        0.00305 ( 8063)
  covalent geometry    : angle       0.70851 (10926)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.6544 (t0) cc_final: 0.6338 (m-40)
REVERT: C  149 ARG cc_start: 0.6132 (tmm160) cc_final: 0.5618 (tpt90)
REVERT: C  172 CYS cc_start: 0.7813 (m) cc_final: 0.6627 (t)
REVERT: C  204 MET cc_start: 0.5089 (ppp) cc_final: 0.4003 (mmt)
REVERT: C  244 MET cc_start: 0.8594 (ppp) cc_final: 0.8358 (ppp)
REVERT: C  246 PHE cc_start: 0.7440 (t80) cc_final: 0.7240 (t80)
REVERT: C  293 MET cc_start: 0.6152 (pmm) cc_final: 0.5157 (ppp)
REVERT: C  301 GLN cc_start: 0.8127 (pm20) cc_final: 0.7369 (tt0)
REVERT: C  321 TRP cc_start: 0.8894 (m100) cc_final: 0.8487 (m100)
REVERT: C  330 MET cc_start: 0.7383 (tpp) cc_final: 0.6983 (ttp)
REVERT: C  348 HIS cc_start: 0.8073 (m90) cc_final: 0.7759 (m90)
REVERT: C  352 MET cc_start: 0.8629 (mmt) cc_final: 0.8309 (mmp)
REVERT: D   12 ILE cc_start: 0.8077 (mp) cc_final: 0.7831 (mt)
REVERT: A   25 GLU cc_start: 0.8802 (pt0) cc_final: 0.8409 (mm-30)
REVERT: A  155 TYR cc_start: 0.8377 (m-80) cc_final: 0.7928 (m-80)
REVERT: A  248 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7763 (pttm)
REVERT: A  251 ASP cc_start: 0.7783 (t0) cc_final: 0.7459 (t0)
REVERT: A  259 PHE cc_start: 0.8819 (m-80) cc_final: 0.8257 (m-80)
REVERT: A  265 ILE cc_start: 0.9119 (mt) cc_final: 0.8846 (mm)
REVERT: A  277 LYS cc_start: 0.7284 (tttt) cc_final: 0.7022 (tttt)
REVERT: A  297 GLU cc_start: 0.8386 (pm20) cc_final: 0.8132 (pm20)
REVERT: A  347 ASN cc_start: 0.8749 (m110) cc_final: 0.8503 (m-40)
REVERT: B  275 SER cc_start: 0.8642 (t) cc_final: 0.8334 (m)
REVERT: B  311 HIS cc_start: 0.7628 (m-70) cc_final: 0.7287 (m-70)
REVERT: G   38 GLU cc_start: 0.8902 (mp0) cc_final: 0.8477 (mm-30)
REVERT: G   41 ARG cc_start: 0.8712 (pmt-80) cc_final: 0.7905 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2136
  time to fit residues: 65.1349
Evaluate side-chains
  166 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 60 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0060
   overall best weight:    2.1802

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 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 = 0.3834 r_free = 0.3834 target = 0.109727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.081826 restraints weight = 86961.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.087118 restraints weight = 34608.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.089444 restraints weight = 15988.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.6684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8064  Z= 0.178
  Angle     :  0.734   8.238  10928  Z= 0.386
  Chirality :  0.046   0.193   1252
  Planarity :  0.004   0.065   1384
  Dihedral  :  4.814  20.106   1092
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.27), residues: 992
  helix:  1.10 (0.24), residues: 452
  sheet: -0.29 (0.40), residues: 167
  loop : -1.20 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.027   0.002   PHE A 108 
 TYR   0.012   0.002   TYR C 324 
 ARG   0.007   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04351 (  423)
  hydrogen bonds       : angle       5.15589 ( 1234)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       1.44737 (    2)
  covalent geometry    : bond        0.00388 ( 8063)
  covalent geometry    : angle       0.73351 (10926)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3482.63 seconds
wall clock time: 63 minutes 57.58 seconds (3837.58 seconds total)