Starting phenix.real_space_refine
on Tue Mar  3 17:57:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0s_23102/03_2026/7l0s_23102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0s_23102/03_2026/7l0s_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_23102/03_2026/7l0s_23102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2026/7l0s_23102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2026/7l0s_23102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2026/7l0s_23102.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.29, per 1000 atoms: 0.29
  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: 0.70
  Conformation dependent library (CDL) restraints added in 387.5 milliseconds
  

  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: 0.37
  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: 1.29

  Time building geometry restraints manager: 0.89 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.950
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.013   0.001   ARG A 176 
 TYR   0.029   0.004   TYR C 349 
 PHE   0.038   0.004   PHE C 376 
 TRP   0.051   0.004   TRP B 297 
 HIS   0.008   0.003   HIS B  54 

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

*********************** 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  : 0.310 
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: C   66 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7200 (pp)
REVERT: C   87 PHE cc_start: 0.5700 (t80) cc_final: 0.5398 (m-10)
REVERT: C  105 TYR cc_start: 0.7591 (m-80) cc_final: 0.7366 (m-80)
REVERT: C  153 THR cc_start: 0.7531 (m) cc_final: 0.7263 (m)
REVERT: C  169 LEU cc_start: 0.8763 (tp) cc_final: 0.8545 (tp)
REVERT: C  325 HIS cc_start: 0.7033 (m-70) cc_final: 0.6002 (m-70)
REVERT: C  376 PHE cc_start: 0.5539 (t80) cc_final: 0.4759 (t80)
REVERT: A   28 GLU cc_start: 0.8283 (tt0) cc_final: 0.7788 (tm-30)
REVERT: B   79 LEU cc_start: 0.9083 (pt) cc_final: 0.8608 (pp)
REVERT: B  149 CYS cc_start: 0.7745 (p) cc_final: 0.7460 (m)
REVERT: B  233 CYS cc_start: 0.7339 (p) cc_final: 0.7002 (p)
REVERT: B  275 SER cc_start: 0.9186 (t) cc_final: 0.8626 (m)
REVERT: B  276 VAL cc_start: 0.8726 (m) cc_final: 0.8463 (m)
REVERT: B  303 ASP cc_start: 0.7234 (t0) cc_final: 0.6718 (t0)
REVERT: B  337 LYS cc_start: 0.8774 (mttm) cc_final: 0.8392 (mptt)
REVERT: G   46 GLU cc_start: 0.8395 (tt0) cc_final: 0.8101 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 322
  average time/residue: 0.0956
  time to fit residues: 40.1092
Evaluate side-chains
  215 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 211
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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
C 292 ASN
A  79 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 142 HIS
B 230 ASN
B 259 GLN
B 295 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.113860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.084272 restraints weight = 80822.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090246 restraints weight = 32579.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.093181 restraints weight = 15995.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.095393 restraints weight = 9651.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.095597 restraints weight = 7396.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8064  Z= 0.159
  Angle     :  0.707   8.670  10928  Z= 0.375
  Chirality :  0.044   0.172   1252
  Planarity :  0.005   0.043   1384
  Dihedral  :  5.463  62.999   1092
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.02 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 992
  helix: -0.14 (0.22), residues: 461
  sheet: -1.68 (0.35), residues: 183
  loop : -1.81 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.014   0.002   TYR B 264 
 PHE   0.022   0.002   PHE A 199 
 TRP   0.025   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8063)
  covalent geometry    : angle       0.70705 (10926)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       1.21182 (    2)
  hydrogen bonds       : bond        0.05073 (  423)
  hydrogen bonds       : angle       5.46840 ( 1234)

*********************** 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
  267 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   87 PHE cc_start: 0.4964 (t80) cc_final: 0.4714 (m-80)
REVERT: C  105 TYR cc_start: 0.7798 (m-80) cc_final: 0.7334 (m-80)
REVERT: C  166 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: C  168 TYR cc_start: 0.7352 (t80) cc_final: 0.6803 (t80)
REVERT: C  169 LEU cc_start: 0.8658 (tp) cc_final: 0.8248 (tp)
REVERT: C  187 LYS cc_start: 0.7582 (mtpt) cc_final: 0.7176 (mttp)
REVERT: C  224 VAL cc_start: 0.6536 (m) cc_final: 0.6279 (m)
REVERT: C  267 MET cc_start: 0.8549 (mtm) cc_final: 0.8293 (mtp)
REVERT: C  330 MET cc_start: 0.7766 (tpp) cc_final: 0.7272 (ttp)
REVERT: A  209 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8504 (ttpp)
REVERT: A  321 THR cc_start: 0.8321 (p) cc_final: 0.7978 (p)
REVERT: B   57 LYS cc_start: 0.8566 (mttt) cc_final: 0.8253 (mtmt)
REVERT: B   61 MET cc_start: 0.7600 (ppp) cc_final: 0.7120 (ppp)
REVERT: B  190 LEU cc_start: 0.9347 (tt) cc_final: 0.9114 (tt)
REVERT: B  225 HIS cc_start: 0.5651 (m-70) cc_final: 0.5430 (m-70)
REVERT: B  233 CYS cc_start: 0.7890 (p) cc_final: 0.7609 (p)
REVERT: B  246 ASP cc_start: 0.8395 (m-30) cc_final: 0.7807 (m-30)
REVERT: B  297 TRP cc_start: 0.6911 (m100) cc_final: 0.6675 (m100)
REVERT: B  317 CYS cc_start: 0.7276 (p) cc_final: 0.6949 (p)
REVERT: B  337 LYS cc_start: 0.8994 (mttm) cc_final: 0.8733 (mptt)
REVERT: G   32 LEU cc_start: 0.8826 (tp) cc_final: 0.8592 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 267
  average time/residue: 0.0823
  time to fit residues: 30.2424
Evaluate side-chains
  193 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0050
   chunk 87 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 69 optimal weight:    0.1980
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN
C 257 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 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 306 GLN
B 311 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.115085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.085643 restraints weight = 83531.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.091280 restraints weight = 36800.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.095958 restraints weight = 16625.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.096800 restraints weight = 9119.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.096741 restraints weight = 8123.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8064  Z= 0.132
  Angle     :  0.657   8.088  10928  Z= 0.347
  Chirality :  0.043   0.218   1252
  Planarity :  0.004   0.043   1384
  Dihedral  :  5.042  54.483   1092
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.25 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.26), residues: 992
  helix:  0.49 (0.23), residues: 462
  sheet: -1.31 (0.36), residues: 170
  loop : -1.59 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  68 
 TYR   0.025   0.002   TYR C 168 
 PHE   0.024   0.002   PHE A 108 
 TRP   0.023   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8063)
  covalent geometry    : angle       0.65692 (10926)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       0.45763 (    2)
  hydrogen bonds       : bond        0.04491 (  423)
  hydrogen bonds       : angle       5.11941 ( 1234)

*********************** 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
  262 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  187 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7248 (mttp)
REVERT: C  267 MET cc_start: 0.8517 (mtm) cc_final: 0.8207 (mtp)
REVERT: C  321 TRP cc_start: 0.8916 (m100) cc_final: 0.8374 (m100)
REVERT: C  330 MET cc_start: 0.7790 (tpp) cc_final: 0.7262 (ttp)
REVERT: A  200 ASP cc_start: 0.7361 (t0) cc_final: 0.6994 (m-30)
REVERT: A  209 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8492 (ttpp)
REVERT: A  248 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8115 (pttm)
REVERT: A  265 ILE cc_start: 0.8868 (mt) cc_final: 0.8603 (mm)
REVERT: B   57 LYS cc_start: 0.8622 (mttt) cc_final: 0.8296 (mtmt)
REVERT: B  225 HIS cc_start: 0.5729 (m-70) cc_final: 0.5432 (m-70)
REVERT: B  246 ASP cc_start: 0.8585 (m-30) cc_final: 0.7821 (m-30)
REVERT: G   38 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8655 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.0812
  time to fit residues: 29.0788
Evaluate side-chains
  177 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0370
   chunk 94 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 59 optimal weight:    0.2980
   chunk 41 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    2.8664

-------------------------------------------------------------------------------
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
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
B 142 HIS
B 175 GLN
B 266 HIS
B 311 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.108697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.078161 restraints weight = 106020.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.082758 restraints weight = 38483.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.085959 restraints weight = 20230.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.088040 restraints weight = 12858.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.089582 restraints weight = 9364.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    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 = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8064  Z= 0.204
  Angle     :  0.707   9.038  10928  Z= 0.373
  Chirality :  0.045   0.146   1252
  Planarity :  0.005   0.069   1384
  Dihedral  :  5.129  47.703   1092
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  4.41 %
    Favored  : 95.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.27), residues: 992
  helix:  0.83 (0.24), residues: 459
  sheet: -0.85 (0.37), residues: 179
  loop : -1.36 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  32 
 TYR   0.015   0.002   TYR B 105 
 PHE   0.022   0.002   PHE A 199 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.007   0.002   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 8063)
  covalent geometry    : angle       0.70569 (10926)
  SS BOND              : bond        0.00438 (    1)
  SS BOND              : angle       2.70100 (    2)
  hydrogen bonds       : bond        0.04548 (  423)
  hydrogen bonds       : angle       5.15863 ( 1234)

*********************** 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
  229 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 226
  time to evaluate  : 0.315 
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  168 TYR cc_start: 0.7300 (t80) cc_final: 0.6704 (t80)
REVERT: C  183 ARG cc_start: 0.5265 (ptp-170) cc_final: 0.5028 (ptp-170)
REVERT: C  204 MET cc_start: 0.6613 (ttp) cc_final: 0.6114 (mmp)
REVERT: C  246 PHE cc_start: 0.7663 (t80) cc_final: 0.7460 (t80)
REVERT: C  267 MET cc_start: 0.8630 (mtm) cc_final: 0.8309 (mtp)
REVERT: C  330 MET cc_start: 0.7703 (tpp) cc_final: 0.7071 (ttp)
REVERT: A  194 LEU cc_start: 0.8450 (tt) cc_final: 0.8194 (mp)
REVERT: A  200 ASP cc_start: 0.7703 (t0) cc_final: 0.7336 (m-30)
REVERT: A  209 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8589 (ttpp)
REVERT: A  248 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8132 (ptpp)
REVERT: A  351 CYS cc_start: 0.8435 (t) cc_final: 0.7801 (t)
REVERT: B   57 LYS cc_start: 0.8993 (mttt) cc_final: 0.8759 (mtmt)
REVERT: B  246 ASP cc_start: 0.8484 (m-30) cc_final: 0.8050 (m-30)
REVERT: B  297 TRP cc_start: 0.6371 (m-10) cc_final: 0.5659 (m-10)
REVERT: B  308 LEU cc_start: 0.9257 (tp) cc_final: 0.8882 (tp)
REVERT: G   31 MET cc_start: 0.2887 (ptp) cc_final: 0.2578 (mpp)
REVERT: G   44 VAL cc_start: 0.9194 (m) cc_final: 0.8973 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0729
  time to fit residues: 23.6869
Evaluate side-chains
  170 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0170
   chunk 25 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    1.8026

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

Flipped N/Q/H residues before XYZ refinement:
C 211 GLN
C 239 GLN
C 241 ASN
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 ASN
B 230 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.110053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.084816 restraints weight = 98122.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.086856 restraints weight = 37926.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.089233 restraints weight = 23067.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.090934 restraints weight = 14867.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.091364 restraints weight = 12490.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    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 = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.5438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8064  Z= 0.162
  Angle     :  0.668   7.370  10928  Z= 0.351
  Chirality :  0.044   0.246   1252
  Planarity :  0.004   0.077   1384
  Dihedral  :  4.972  39.719   1092
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  2.90 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.28), residues: 992
  helix:  0.90 (0.24), residues: 463
  sheet: -0.83 (0.38), residues: 184
  loop : -1.17 (0.36), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  32 
 TYR   0.022   0.002   TYR C 168 
 PHE   0.034   0.002   PHE A 108 
 TRP   0.032   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8063)
  covalent geometry    : angle       0.66739 (10926)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       1.15998 (    2)
  hydrogen bonds       : bond        0.04443 (  423)
  hydrogen bonds       : angle       5.02847 ( 1234)

*********************** 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
  221 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 218
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  153 THR cc_start: 0.7629 (p) cc_final: 0.7174 (p)
REVERT: C  166 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7948 (tm-30)
REVERT: C  168 TYR cc_start: 0.7563 (t80) cc_final: 0.7296 (t80)
REVERT: C  183 ARG cc_start: 0.5304 (ptp-170) cc_final: 0.4980 (ptp-170)
REVERT: C  246 PHE cc_start: 0.7562 (t80) cc_final: 0.7346 (t80)
REVERT: C  267 MET cc_start: 0.8616 (mtm) cc_final: 0.8300 (mtp)
REVERT: C  330 MET cc_start: 0.7598 (tpp) cc_final: 0.7218 (ttp)
REVERT: C  359 TYR cc_start: 0.6894 (m-80) cc_final: 0.6441 (m-10)
REVERT: D   12 ILE cc_start: 0.8168 (mp) cc_final: 0.7804 (mt)
REVERT: A  194 LEU cc_start: 0.8770 (tt) cc_final: 0.8263 (mp)
REVERT: A  200 ASP cc_start: 0.7535 (t0) cc_final: 0.7156 (m-30)
REVERT: A  209 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8603 (ttpp)
REVERT: A  248 LYS cc_start: 0.8365 (ptpp) cc_final: 0.8036 (pttm)
REVERT: B   57 LYS cc_start: 0.8916 (mttt) cc_final: 0.8603 (mtmt)
REVERT: B   78 LYS cc_start: 0.7104 (mmpt) cc_final: 0.6801 (mmmt)
REVERT: B  246 ASP cc_start: 0.8546 (m-30) cc_final: 0.8255 (m-30)
REVERT: B  297 TRP cc_start: 0.5919 (m-10) cc_final: 0.5608 (m-10)
REVERT: B  308 LEU cc_start: 0.9321 (tp) cc_final: 0.8999 (tp)
REVERT: B  311 HIS cc_start: 0.7053 (m-70) cc_final: 0.6533 (m-70)
REVERT: G   31 MET cc_start: 0.2614 (ptp) cc_final: 0.2303 (mpp)
REVERT: G   38 GLU cc_start: 0.8713 (mp0) cc_final: 0.8252 (mp0)
  outliers start: 3
  outliers final: 1
  residues processed: 221
  average time/residue: 0.0762
  time to fit residues: 23.3183
Evaluate side-chains
  165 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 63 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  52 GLN
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.110098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.083684 restraints weight = 91382.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.086703 restraints weight = 34207.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.089306 restraints weight = 19180.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.090363 restraints weight = 12908.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.090846 restraints weight = 11477.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.5801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8064  Z= 0.156
  Angle     :  0.667   7.516  10928  Z= 0.350
  Chirality :  0.044   0.165   1252
  Planarity :  0.005   0.076   1384
  Dihedral  :  4.845  32.140   1092
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.02 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.27), residues: 992
  helix:  0.98 (0.24), residues: 456
  sheet: -0.72 (0.38), residues: 184
  loop : -1.16 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.018   0.002   TYR C 333 
 PHE   0.028   0.002   PHE A 108 
 TRP   0.039   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8063)
  covalent geometry    : angle       0.66718 (10926)
  SS BOND              : bond        0.00762 (    1)
  SS BOND              : angle       0.91446 (    2)
  hydrogen bonds       : bond        0.04452 (  423)
  hydrogen bonds       : angle       4.98170 ( 1234)

*********************** 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
  224 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.299 
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  168 TYR cc_start: 0.7632 (t80) cc_final: 0.7265 (t80)
REVERT: C  246 PHE cc_start: 0.7543 (t80) cc_final: 0.7274 (t80)
REVERT: C  267 MET cc_start: 0.8686 (mtm) cc_final: 0.8311 (mtp)
REVERT: C  293 MET cc_start: 0.6195 (pmm) cc_final: 0.5160 (ppp)
REVERT: C  330 MET cc_start: 0.7778 (tpp) cc_final: 0.7280 (ttp)
REVERT: C  336 ASP cc_start: 0.8343 (t70) cc_final: 0.7916 (t70)
REVERT: D   12 ILE cc_start: 0.8021 (mp) cc_final: 0.7745 (mt)
REVERT: A  200 ASP cc_start: 0.7728 (t0) cc_final: 0.7153 (m-30)
REVERT: A  209 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8629 (ttpp)
REVERT: A  259 PHE cc_start: 0.8890 (m-80) cc_final: 0.8568 (m-80)
REVERT: A  297 GLU cc_start: 0.8191 (pm20) cc_final: 0.7928 (pm20)
REVERT: B  246 ASP cc_start: 0.8621 (m-30) cc_final: 0.8144 (m-30)
REVERT: B  261 LEU cc_start: 0.9374 (tt) cc_final: 0.9020 (tt)
REVERT: B  308 LEU cc_start: 0.9388 (tp) cc_final: 0.9153 (tp)
REVERT: G   31 MET cc_start: 0.2514 (ptp) cc_final: 0.2245 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 224
  average time/residue: 0.0806
  time to fit residues: 25.0491
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  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.110188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082591 restraints weight = 82642.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.086456 restraints weight = 32109.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.089127 restraints weight = 17021.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.090047 restraints weight = 11604.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.090536 restraints weight = 10818.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    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 = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.6037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8064  Z= 0.160
  Angle     :  0.694   7.698  10928  Z= 0.364
  Chirality :  0.045   0.235   1252
  Planarity :  0.004   0.077   1384
  Dihedral  :  4.723  25.126   1092
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.28), residues: 992
  helix:  1.03 (0.24), residues: 462
  sheet: -0.40 (0.40), residues: 176
  loop : -1.18 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.019   0.002   TYR B 289 
 PHE   0.026   0.002   PHE A 108 
 TRP   0.044   0.002   TRP B 339 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8063)
  covalent geometry    : angle       0.69433 (10926)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       0.58909 (    2)
  hydrogen bonds       : bond        0.04407 (  423)
  hydrogen bonds       : angle       5.02524 ( 1234)

*********************** 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
  220 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8384 (tm-30)
REVERT: C  168 TYR cc_start: 0.7612 (t80) cc_final: 0.7317 (t80)
REVERT: C  246 PHE cc_start: 0.7480 (t80) cc_final: 0.7212 (t80)
REVERT: C  267 MET cc_start: 0.8663 (mtm) cc_final: 0.8298 (mtp)
REVERT: C  293 MET cc_start: 0.6070 (pmm) cc_final: 0.5140 (ppp)
REVERT: C  301 GLN cc_start: 0.7920 (pm20) cc_final: 0.7041 (tt0)
REVERT: C  330 MET cc_start: 0.7650 (tpp) cc_final: 0.7109 (ttp)
REVERT: C  336 ASP cc_start: 0.8445 (t70) cc_final: 0.8148 (t70)
REVERT: C  359 TYR cc_start: 0.7000 (m-80) cc_final: 0.6624 (m-10)
REVERT: D   12 ILE cc_start: 0.7857 (mp) cc_final: 0.7579 (mt)
REVERT: A  155 TYR cc_start: 0.8699 (m-80) cc_final: 0.8076 (m-80)
REVERT: A  200 ASP cc_start: 0.7685 (t0) cc_final: 0.7140 (m-30)
REVERT: A  209 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8587 (ttpp)
REVERT: A  248 LYS cc_start: 0.8339 (ptpp) cc_final: 0.7998 (pttm)
REVERT: A  259 PHE cc_start: 0.8823 (m-80) cc_final: 0.8520 (m-80)
REVERT: A  297 GLU cc_start: 0.8181 (pm20) cc_final: 0.7930 (pm20)
REVERT: B   85 TYR cc_start: 0.8954 (m-80) cc_final: 0.8298 (m-80)
REVERT: B  246 ASP cc_start: 0.8723 (m-30) cc_final: 0.8240 (m-30)
REVERT: B  331 SER cc_start: 0.8959 (p) cc_final: 0.8749 (p)
REVERT: G   38 GLU cc_start: 0.8863 (mp0) cc_final: 0.8454 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0765
  time to fit residues: 23.6613
Evaluate side-chains
  160 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0570
   chunk 70 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
A  22 ASN
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.112834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.085815 restraints weight = 89123.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.089599 restraints weight = 34159.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.092236 restraints weight = 18501.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.093236 restraints weight = 12499.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.093724 restraints weight = 11492.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    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 = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.6357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8064  Z= 0.131
  Angle     :  0.685  12.423  10928  Z= 0.353
  Chirality :  0.044   0.237   1252
  Planarity :  0.004   0.075   1384
  Dihedral  :  4.641  24.458   1092
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.28), residues: 992
  helix:  1.30 (0.24), residues: 456
  sheet: -0.17 (0.40), residues: 172
  loop : -1.28 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  47 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.025   0.001   PHE A 108 
 TRP   0.043   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8063)
  covalent geometry    : angle       0.68480 (10926)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.53396 (    2)
  hydrogen bonds       : bond        0.04201 (  423)
  hydrogen bonds       : angle       4.86721 ( 1234)

*********************** 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
  221 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  149 ARG cc_start: 0.5483 (tmm160) cc_final: 0.5221 (tpt90)
REVERT: C  153 THR cc_start: 0.6960 (p) cc_final: 0.6384 (p)
REVERT: C  166 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: C  246 PHE cc_start: 0.7423 (t80) cc_final: 0.7164 (t80)
REVERT: C  267 MET cc_start: 0.8605 (mtm) cc_final: 0.8345 (mtp)
REVERT: C  293 MET cc_start: 0.5865 (pmm) cc_final: 0.4857 (ppp)
REVERT: C  301 GLN cc_start: 0.7965 (pm20) cc_final: 0.7098 (tt0)
REVERT: C  330 MET cc_start: 0.7579 (tpp) cc_final: 0.7093 (ttp)
REVERT: D   12 ILE cc_start: 0.7728 (mp) cc_final: 0.7397 (mt)
REVERT: A  194 LEU cc_start: 0.8585 (tt) cc_final: 0.8174 (mp)
REVERT: A  200 ASP cc_start: 0.7501 (t0) cc_final: 0.6931 (m-30)
REVERT: A  209 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8531 (ttpp)
REVERT: A  248 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7907 (pttm)
REVERT: A  259 PHE cc_start: 0.8705 (m-80) cc_final: 0.8188 (m-80)
REVERT: A  265 ILE cc_start: 0.9041 (mt) cc_final: 0.8797 (mm)
REVERT: B   75 GLN cc_start: 0.8716 (mp10) cc_final: 0.7966 (mp10)
REVERT: B   85 TYR cc_start: 0.8797 (m-80) cc_final: 0.8347 (m-80)
REVERT: B  246 ASP cc_start: 0.8777 (m-30) cc_final: 0.8358 (m-30)
REVERT: B  332 TRP cc_start: 0.8679 (m-10) cc_final: 0.7429 (m-10)
REVERT: B  339 TRP cc_start: 0.6877 (m100) cc_final: 0.6395 (m100)
REVERT: B  340 ASN cc_start: 0.4466 (m-40) cc_final: 0.4074 (m110)
REVERT: G   35 LYS cc_start: 0.9044 (pttt) cc_final: 0.8385 (pptt)
REVERT: G   38 GLU cc_start: 0.8713 (mp0) cc_final: 0.8200 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0754
  time to fit residues: 23.6291
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  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 86 optimal weight:    0.4980
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.112104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.084211 restraints weight = 78504.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.089048 restraints weight = 33858.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.092689 restraints weight = 15706.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.092934 restraints weight = 9593.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.093304 restraints weight = 9234.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    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 = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.6480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8064  Z= 0.135
  Angle     :  0.690   9.179  10928  Z= 0.356
  Chirality :  0.044   0.138   1252
  Planarity :  0.004   0.050   1384
  Dihedral  :  4.637  20.679   1092
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.28), residues: 992
  helix:  1.28 (0.24), residues: 456
  sheet: -0.07 (0.40), residues: 168
  loop : -1.25 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  47 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.025   0.002   PHE B 241 
 TRP   0.042   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8063)
  covalent geometry    : angle       0.69041 (10926)
  SS BOND              : bond        0.00458 (    1)
  SS BOND              : angle       0.79415 (    2)
  hydrogen bonds       : bond        0.04187 (  423)
  hydrogen bonds       : angle       4.86237 ( 1234)

*********************** 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
  215 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  153 THR cc_start: 0.7022 (p) cc_final: 0.6214 (p)
REVERT: C  166 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: C  168 TYR cc_start: 0.7835 (t80) cc_final: 0.7472 (t80)
REVERT: C  204 MET cc_start: 0.4870 (ppp) cc_final: 0.3852 (mmt)
REVERT: C  246 PHE cc_start: 0.7438 (t80) cc_final: 0.7170 (t80)
REVERT: C  267 MET cc_start: 0.8595 (mtm) cc_final: 0.8332 (mtp)
REVERT: C  293 MET cc_start: 0.5815 (pmm) cc_final: 0.4925 (ppp)
REVERT: C  330 MET cc_start: 0.7423 (tpp) cc_final: 0.7014 (ttp)
REVERT: D   12 ILE cc_start: 0.7677 (mp) cc_final: 0.7289 (mt)
REVERT: A  155 TYR cc_start: 0.8613 (m-80) cc_final: 0.8168 (m-10)
REVERT: A  194 LEU cc_start: 0.8257 (tt) cc_final: 0.7951 (mt)
REVERT: A  200 ASP cc_start: 0.7456 (t0) cc_final: 0.6924 (m-30)
REVERT: A  209 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8466 (ttpp)
REVERT: A  248 LYS cc_start: 0.8214 (ptpp) cc_final: 0.7871 (pttm)
REVERT: A  259 PHE cc_start: 0.8709 (m-80) cc_final: 0.8416 (m-80)
REVERT: A  265 ILE cc_start: 0.9088 (mt) cc_final: 0.8835 (mm)
REVERT: A  297 GLU cc_start: 0.8182 (pm20) cc_final: 0.7942 (pm20)
REVERT: B   75 GLN cc_start: 0.8723 (mp10) cc_final: 0.7945 (mp10)
REVERT: B   85 TYR cc_start: 0.8909 (m-80) cc_final: 0.8323 (m-80)
REVERT: B  100 VAL cc_start: 0.8828 (t) cc_final: 0.8615 (m)
REVERT: B  190 LEU cc_start: 0.9171 (tt) cc_final: 0.8924 (tt)
REVERT: B  246 ASP cc_start: 0.8813 (m-30) cc_final: 0.8318 (m-30)
REVERT: B  329 THR cc_start: 0.8452 (p) cc_final: 0.7832 (p)
REVERT: B  332 TRP cc_start: 0.8694 (m-10) cc_final: 0.7609 (m-10)
REVERT: B  339 TRP cc_start: 0.7037 (m100) cc_final: 0.6597 (m100)
REVERT: G   35 LYS cc_start: 0.9061 (pttt) cc_final: 0.8555 (pptt)
REVERT: G   38 GLU cc_start: 0.8653 (mp0) cc_final: 0.8192 (mp0)
REVERT: G   60 ASP cc_start: 0.8127 (p0) cc_final: 0.7715 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0780
  time to fit residues: 23.4153
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  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
C 270 GLN
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
B 230 ASN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.111232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.085519 restraints weight = 96256.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.088361 restraints weight = 37556.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.089986 restraints weight = 23190.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.091636 restraints weight = 15905.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.092088 restraints weight = 13253.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    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 = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.6653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8064  Z= 0.151
  Angle     :  0.728  12.377  10928  Z= 0.373
  Chirality :  0.046   0.358   1252
  Planarity :  0.004   0.048   1384
  Dihedral  :  4.722  19.749   1092
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.28), residues: 992
  helix:  1.33 (0.24), residues: 456
  sheet: -0.23 (0.39), residues: 176
  loop : -1.17 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  47 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.024   0.002   PHE A 108 
 TRP   0.045   0.002   TRP B 339 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8063)
  covalent geometry    : angle       0.72592 (10926)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       4.16701 (    2)
  hydrogen bonds       : bond        0.04282 (  423)
  hydrogen bonds       : angle       5.01247 ( 1234)

********************** 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
  209 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: C  204 MET cc_start: 0.5124 (ppp) cc_final: 0.3921 (mmt)
REVERT: C  246 PHE cc_start: 0.7471 (t80) cc_final: 0.7166 (t80)
REVERT: C  256 LEU cc_start: 0.7409 (mt) cc_final: 0.7087 (mp)
REVERT: C  293 MET cc_start: 0.5889 (pmm) cc_final: 0.5010 (ppp)
REVERT: C  301 GLN cc_start: 0.8006 (pm20) cc_final: 0.7103 (tt0)
REVERT: C  330 MET cc_start: 0.7441 (tpp) cc_final: 0.7042 (ttp)
REVERT: C  348 HIS cc_start: 0.8087 (m90) cc_final: 0.7790 (m90)
REVERT: D   12 ILE cc_start: 0.7714 (mp) cc_final: 0.7288 (mt)
REVERT: A  155 TYR cc_start: 0.8524 (m-80) cc_final: 0.8106 (m-10)
REVERT: A  194 LEU cc_start: 0.8647 (tt) cc_final: 0.8146 (mp)
REVERT: A  209 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8491 (ttpp)
REVERT: A  259 PHE cc_start: 0.8761 (m-80) cc_final: 0.8462 (m-80)
REVERT: A  265 ILE cc_start: 0.8895 (mt) cc_final: 0.8570 (mm)
REVERT: B   75 GLN cc_start: 0.8762 (mp10) cc_final: 0.8125 (mp10)
REVERT: B   85 TYR cc_start: 0.8849 (m-80) cc_final: 0.8331 (m-80)
REVERT: B  246 ASP cc_start: 0.8731 (m-30) cc_final: 0.8301 (m-30)
REVERT: B  311 HIS cc_start: 0.7023 (m-70) cc_final: 0.6612 (m-70)
REVERT: B  329 THR cc_start: 0.8533 (p) cc_final: 0.8128 (p)
REVERT: B  339 TRP cc_start: 0.6974 (m100) cc_final: 0.6630 (m100)
REVERT: G   35 LYS cc_start: 0.9072 (pttt) cc_final: 0.8433 (pptt)
REVERT: G   38 GLU cc_start: 0.8649 (mp0) cc_final: 0.8234 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0705
  time to fit residues: 21.2270
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  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0170
   chunk 66 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.4980
   chunk 20 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.4220

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** B 340 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 = 0.3850 r_free = 0.3850 target = 0.110887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.083854 restraints weight = 107228.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.088284 restraints weight = 44175.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.089987 restraints weight = 23926.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.092037 restraints weight = 16956.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.092429 restraints weight = 13581.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    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 = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.6703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8064  Z= 0.149
  Angle     :  0.720   9.866  10928  Z= 0.370
  Chirality :  0.045   0.295   1252
  Planarity :  0.005   0.081   1384
  Dihedral  :  4.747  22.134   1092
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.28), residues: 992
  helix:  1.27 (0.24), residues: 456
  sheet: -0.29 (0.39), residues: 176
  loop : -1.13 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 149 
 TYR   0.020   0.001   TYR B 289 
 PHE   0.024   0.002   PHE A 108 
 TRP   0.041   0.002   TRP B 339 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8063)
  covalent geometry    : angle       0.71847 (10926)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       3.99224 (    2)
  hydrogen bonds       : bond        0.04272 (  423)
  hydrogen bonds       : angle       5.00876 ( 1234)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1518.37 seconds
wall clock time: 27 minutes 0.02 seconds (1620.02 seconds total)