Starting phenix.real_space_refine
on Wed Mar 12 11:10:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0s_23102/03_2025/7l0s_23102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0s_23102/03_2025/7l0s_23102.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2025/7l0s_23102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2025/7l0s_23102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2025/7l0s_23102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0s_23102/03_2025/7l0s_23102.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5034      2.51       5
     N    1343      2.21       5
     O    1472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7906
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 2424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2424
          Classifications: {'peptide': 308}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 297}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 2729
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 337, 2694
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 4, 'TRANS': 332}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 337, 2694
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 4, 'TRANS': 332}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 2697
    Chain: "B"
      Number of atoms: 2385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2385
          Classifications: {'peptide': 311}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 305}
    Chain: "G"
      Number of atoms: 310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 310
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 3, 'TRANS': 35}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AASP A  97 " occ=0.56
      ... (14 atoms not shown)
      pdb=" OD2BASP A  97 " occ=0.44
    residue:
      pdb=" N  AARG A 105 " occ=0.68
      ... (20 atoms not shown)
      pdb=" NH2BARG A 105 " occ=0.32
    residue:
      pdb=" N  AASP A 158 " occ=0.51
      ... (14 atoms not shown)
      pdb=" OD2BASP A 158 " occ=0.49
    residue:
      pdb=" N  AASP A 160 " occ=0.44
      ... (14 atoms not shown)
      pdb=" OD2BASP A 160 " occ=0.56
  Time building chain proxies: 6.36, per 1000 atoms: 0.80
  Number of scatterers: 7906
  At special positions: 0
  Unit cell: (88.275, 117.15, 121.275, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1472      8.00
     N    1343      7.00
     C    5034      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.02
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      48.2% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'C' and resid 60 through 91
    Processing helix  chain 'C' and resid 100 through 129
      Proline residue:  C 122  - end of helix
    Processing helix  chain 'C' and resid 137 through 173
    Processing helix  chain 'C' and resid 173 through 181
    Processing helix  chain 'C' and resid 182 through 202
    Processing helix  chain 'C' and resid 202 through 207
      removed outlier: 3.519A  pdb=" N   THR C 207 " --> pdb=" O   PRO C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 270
      Proline residue:  C 249  - end of helix
    Processing helix  chain 'C' and resid 300 through 334
      Proline residue:  C 323  - end of helix
      removed outlier: 3.533A  pdb=" N   ILE C 334 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 371
      Proline residue:  C 366  - end of helix
    Processing helix  chain 'C' and resid 373 through 385
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.507A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 65 through 68
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.598A  pdb=" N   GLY A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 114
      removed outlier: 3.851A  pdb=" N   ASP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 133
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.541A  pdb=" N  AASP A 158 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.781A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.404A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'G' and resid 32 through 48
    Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190
      removed outlier: 6.527A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.895A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.837A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.974A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.399A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.062A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.903A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1234 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 2.39 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.32 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.360
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.010
-------------------------------------------------------------------------------
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   8063  Z= 0.524
  Angle     :  1.345  11.500  10926  Z= 0.786
  Chirality :  0.079   0.410   1252
  Planarity :  0.008   0.061   1384
  Dihedral  : 13.518  70.452   2896
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.80 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.22), residues: 992
  helix: -1.81 (0.19), residues: 461
  sheet: -2.25 (0.36), residues: 173
  loop : -2.15 (0.29), residues: 358

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

*********************** 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  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7195 (pp)
REVERT: C   87 PHE cc_start: 0.5700 (t80) cc_final: 0.5394 (m-10)
REVERT: C  105 TYR cc_start: 0.7591 (m-80) cc_final: 0.7375 (m-80)
REVERT: C  153 THR cc_start: 0.7532 (m) cc_final: 0.7254 (m)
REVERT: C  169 LEU cc_start: 0.8763 (tp) cc_final: 0.8547 (tp)
REVERT: C  242 THR cc_start: 0.8417 (t) cc_final: 0.8115 (t)
REVERT: C  325 HIS cc_start: 0.7032 (m-70) cc_final: 0.5956 (m-70)
REVERT: C  376 PHE cc_start: 0.5539 (t80) cc_final: 0.4751 (t80)
REVERT: A   28 GLU cc_start: 0.8284 (tt0) cc_final: 0.7792 (tm-30)
REVERT: B   79 LEU cc_start: 0.9083 (pt) cc_final: 0.8600 (pp)
REVERT: B  149 CYS cc_start: 0.7744 (p) cc_final: 0.7450 (m)
REVERT: B  233 CYS cc_start: 0.7340 (p) cc_final: 0.7044 (p)
REVERT: B  275 SER cc_start: 0.9186 (t) cc_final: 0.8629 (m)
REVERT: B  276 VAL cc_start: 0.8726 (m) cc_final: 0.8477 (m)
REVERT: B  329 THR cc_start: 0.8680 (t) cc_final: 0.8475 (t)
REVERT: B  337 LYS cc_start: 0.8774 (mttm) cc_final: 0.8372 (mptt)
REVERT: G   32 LEU cc_start: 0.8607 (tp) cc_final: 0.8281 (tp)
REVERT: G   37 CYS cc_start: 0.7880 (p) cc_final: 0.6775 (p)
REVERT: G   46 GLU cc_start: 0.8395 (tt0) cc_final: 0.7607 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 322
  average time/residue: 0.2992
  time to fit residues: 125.8083
Evaluate side-chains
  216 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 212
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    3.9990

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

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

Total number of N/Q/H flips: 14

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8063  Z= 0.346
  Angle     :  0.792   9.759  10926  Z= 0.426
  Chirality :  0.047   0.169   1252
  Planarity :  0.005   0.046   1384
  Dihedral  :  5.704  61.534   1092
  Min Nonbonded Distance : 2.504

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

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

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

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

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 235
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: C  168 TYR cc_start: 0.7409 (t80) cc_final: 0.6904 (t80)
REVERT: C  169 LEU cc_start: 0.8754 (tp) cc_final: 0.8323 (tp)
REVERT: C  246 PHE cc_start: 0.8007 (t80) cc_final: 0.7803 (t80)
REVERT: C  267 MET cc_start: 0.8633 (mtm) cc_final: 0.8294 (mtp)
REVERT: C  325 HIS cc_start: 0.8332 (m-70) cc_final: 0.8123 (m-70)
REVERT: C  330 MET cc_start: 0.7822 (tpp) cc_final: 0.7280 (ttp)
REVERT: C  350 PHE cc_start: 0.8706 (t80) cc_final: 0.8497 (t80)
REVERT: A   18 MET cc_start: 0.8360 (tmm) cc_final: 0.8151 (tmm)
REVERT: A   32 ARG cc_start: 0.8150 (tpm170) cc_final: 0.7938 (tpm170)
REVERT: A  209 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8647 (ttpp)
REVERT: A  259 PHE cc_start: 0.8810 (m-80) cc_final: 0.8599 (m-80)
REVERT: B   57 LYS cc_start: 0.8901 (mttt) cc_final: 0.8676 (mtmt)
REVERT: B  146 LEU cc_start: 0.9108 (mp) cc_final: 0.8732 (mt)
REVERT: B  149 CYS cc_start: 0.7896 (p) cc_final: 0.7634 (m)
REVERT: B  213 VAL cc_start: 0.7825 (t) cc_final: 0.7078 (p)
REVERT: B  233 CYS cc_start: 0.7975 (p) cc_final: 0.7657 (p)
REVERT: B  246 ASP cc_start: 0.8344 (m-30) cc_final: 0.7918 (m-30)
REVERT: B  337 LYS cc_start: 0.9094 (mttm) cc_final: 0.8703 (mptt)
REVERT: G   34 SER cc_start: 0.8766 (m) cc_final: 0.8449 (m)
REVERT: G   37 CYS cc_start: 0.8524 (p) cc_final: 0.7835 (p)
REVERT: G   38 GLU cc_start: 0.8949 (mp0) cc_final: 0.8586 (mm-30)
REVERT: G   41 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8444 (ttp80)
REVERT: G   42 ASP cc_start: 0.8187 (p0) cc_final: 0.7951 (p0)
  outliers start: 4
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1975
  time to fit residues: 63.0427
Evaluate side-chains
  174 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0870
   chunk 57 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.3162

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.111042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.084125 restraints weight = 94012.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.087756 restraints weight = 35144.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.090861 restraints weight = 18879.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3425
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8063  Z= 0.198
  Angle     :  0.682   7.418  10926  Z= 0.366
  Chirality :  0.045   0.290   1252
  Planarity :  0.004   0.047   1384
  Dihedral  :  5.177  55.863   1092
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.26), residues: 992
  helix:  0.30 (0.23), residues: 464
  sheet: -1.37 (0.36), residues: 187
  loop : -1.24 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 339 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.026   0.002   PHE A 108 
 TYR   0.028   0.002   TYR C 168 
 ARG   0.004   0.001   ARG C 167 

*********************** 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
  250 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.977 
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   99 GLN cc_start: 0.7256 (tp40) cc_final: 0.6964 (tp-100)
REVERT: C  105 TYR cc_start: 0.7133 (m-80) cc_final: 0.6905 (m-80)
REVERT: C  121 MET cc_start: 0.8333 (tpt) cc_final: 0.7709 (tpt)
REVERT: C  168 TYR cc_start: 0.7635 (t80) cc_final: 0.7421 (t80)
REVERT: C  267 MET cc_start: 0.8619 (mtm) cc_final: 0.8235 (mtm)
REVERT: C  321 TRP cc_start: 0.9050 (m100) cc_final: 0.8566 (m100)
REVERT: C  330 MET cc_start: 0.7834 (tpp) cc_final: 0.7187 (ttp)
REVERT: C  352 MET cc_start: 0.8643 (mmt) cc_final: 0.8248 (mmp)
REVERT: C  359 TYR cc_start: 0.7212 (m-10) cc_final: 0.6589 (m-10)
REVERT: D   11 TYR cc_start: 0.7692 (p90) cc_final: 0.7385 (p90)
REVERT: A   18 MET cc_start: 0.8357 (tmm) cc_final: 0.8135 (tmm)
REVERT: A   32 ARG cc_start: 0.7950 (tpm170) cc_final: 0.7663 (tpm170)
REVERT: A  209 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8587 (ttpp)
REVERT: A  259 PHE cc_start: 0.8800 (m-80) cc_final: 0.8555 (m-80)
REVERT: A  265 ILE cc_start: 0.8909 (mt) cc_final: 0.8614 (mm)
REVERT: B   57 LYS cc_start: 0.8884 (mttt) cc_final: 0.8471 (mtmt)
REVERT: B   75 GLN cc_start: 0.8681 (mm110) cc_final: 0.8444 (mm110)
REVERT: B  114 CYS cc_start: 0.5940 (p) cc_final: 0.5516 (m)
REVERT: B  210 LEU cc_start: 0.9420 (tt) cc_final: 0.9162 (tt)
REVERT: B  246 ASP cc_start: 0.8534 (m-30) cc_final: 0.7786 (m-30)
REVERT: G   37 CYS cc_start: 0.8337 (p) cc_final: 0.7890 (p)
REVERT: G   38 GLU cc_start: 0.8916 (mp0) cc_final: 0.8493 (mm-30)
REVERT: G   41 ARG cc_start: 0.8743 (pmt-80) cc_final: 0.7802 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.2132
  time to fit residues: 73.3293
Evaluate side-chains
  164 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 95 optimal weight:    8.9990
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0030
   chunk 91 optimal weight:    8.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 257 ASN
C 262 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.111303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.085352 restraints weight = 112727.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.089988 restraints weight = 43602.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.091695 restraints weight = 21491.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3474
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    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 = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3474
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.4968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8063  Z= 0.187
  Angle     :  0.643   7.202  10926  Z= 0.345
  Chirality :  0.044   0.172   1252
  Planarity :  0.004   0.048   1384
  Dihedral  :  4.868  49.648   1092
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.27), residues: 992
  helix:  0.85 (0.24), residues: 458
  sheet: -0.91 (0.38), residues: 184
  loop : -1.25 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.018   0.001   PHE A 199 
 TYR   0.018   0.002   TYR B 124 
 ARG   0.003   0.000   ARG C 328 

*********************** 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
  230 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.907 
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  168 TYR cc_start: 0.7502 (t80) cc_final: 0.7201 (t80)
REVERT: C  181 MET cc_start: 0.6813 (mmt) cc_final: 0.6540 (mmt)
REVERT: C  224 VAL cc_start: 0.6349 (m) cc_final: 0.6117 (m)
REVERT: C  267 MET cc_start: 0.8574 (mtm) cc_final: 0.8279 (mtm)
REVERT: C  321 TRP cc_start: 0.8966 (m100) cc_final: 0.8454 (m100)
REVERT: C  330 MET cc_start: 0.7673 (tpp) cc_final: 0.7116 (ttp)
REVERT: C  336 ASP cc_start: 0.8989 (t0) cc_final: 0.8655 (t70)
REVERT: C  359 TYR cc_start: 0.7044 (m-10) cc_final: 0.6672 (m-80)
REVERT: A   32 ARG cc_start: 0.7656 (tpm170) cc_final: 0.7357 (tpm170)
REVERT: A  209 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8619 (ttpp)
REVERT: A  248 LYS cc_start: 0.8385 (ptpp) cc_final: 0.8035 (pttm)
REVERT: A  259 PHE cc_start: 0.8761 (m-80) cc_final: 0.8501 (m-80)
REVERT: B   57 LYS cc_start: 0.8820 (mttt) cc_final: 0.8257 (mtmt)
REVERT: B  246 ASP cc_start: 0.8670 (m-30) cc_final: 0.8059 (m-30)
REVERT: B  297 TRP cc_start: 0.7141 (m100) cc_final: 0.6903 (m-10)
REVERT: B  308 LEU cc_start: 0.9255 (tp) cc_final: 0.9016 (tp)
REVERT: B  337 LYS cc_start: 0.8894 (mptt) cc_final: 0.8627 (mptt)
REVERT: B  339 TRP cc_start: 0.7725 (m100) cc_final: 0.7496 (m100)
REVERT: G   37 CYS cc_start: 0.8033 (p) cc_final: 0.7590 (p)
REVERT: G   38 GLU cc_start: 0.8872 (mp0) cc_final: 0.8372 (mm-30)
REVERT: G   41 ARG cc_start: 0.8764 (pmt-80) cc_final: 0.7766 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2068
  time to fit residues: 65.2844
Evaluate side-chains
  174 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
B 132 ASN
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.107873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.077983 restraints weight = 94487.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.082491 restraints weight = 34788.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.085568 restraints weight = 18488.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.5412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8063  Z= 0.245
  Angle     :  0.688   7.293  10926  Z= 0.366
  Chirality :  0.044   0.225   1252
  Planarity :  0.004   0.057   1384
  Dihedral  :  4.977  39.888   1092
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 992
  helix:  0.80 (0.24), residues: 465
  sheet: -0.56 (0.39), residues: 177
  loop : -1.31 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 339 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.018   0.002   PHE A 199 
 TYR   0.027   0.002   TYR B 124 
 ARG   0.007   0.001   ARG C 149 

*********************** 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
  216 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.969 
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  166 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: C  267 MET cc_start: 0.8693 (mtm) cc_final: 0.8326 (mtp)
REVERT: C  321 TRP cc_start: 0.9055 (m100) cc_final: 0.8381 (m100)
REVERT: C  330 MET cc_start: 0.7572 (tpp) cc_final: 0.7009 (ttp)
REVERT: C  336 ASP cc_start: 0.8998 (t0) cc_final: 0.8706 (t70)
REVERT: C  352 MET cc_start: 0.8649 (mmt) cc_final: 0.8235 (mmt)
REVERT: C  359 TYR cc_start: 0.7264 (m-10) cc_final: 0.6918 (m-10)
REVERT: A   32 ARG cc_start: 0.7839 (tpm170) cc_final: 0.7502 (tpm170)
REVERT: A  196 PHE cc_start: 0.8358 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  200 ASP cc_start: 0.7933 (t0) cc_final: 0.7413 (m-30)
REVERT: A  209 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8696 (ttpp)
REVERT: A  259 PHE cc_start: 0.8957 (m-80) cc_final: 0.8382 (m-80)
REVERT: B   57 LYS cc_start: 0.8866 (mttt) cc_final: 0.7737 (mtmt)
REVERT: B   75 GLN cc_start: 0.8721 (mp-120) cc_final: 0.7907 (mp10)
REVERT: B  246 ASP cc_start: 0.8709 (m-30) cc_final: 0.8079 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1730
  time to fit residues: 52.7056
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  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  52 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B  91 HIS
** B 176 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.110665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.082689 restraints weight = 93846.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.087659 restraints weight = 34361.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.090831 restraints weight = 16283.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8063  Z= 0.197
  Angle     :  0.656   7.940  10926  Z= 0.345
  Chirality :  0.043   0.176   1252
  Planarity :  0.004   0.047   1384
  Dihedral  :  4.698  29.632   1092
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.21 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.28), residues: 992
  helix:  0.93 (0.24), residues: 464
  sheet: -0.30 (0.41), residues: 177
  loop : -1.30 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.016   0.001   PHE B 278 
 TYR   0.012   0.001   TYR B 124 
 ARG   0.004   0.000   ARG C 149 

*********************** 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
  226 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.983 
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  121 MET cc_start: 0.8151 (tpt) cc_final: 0.7453 (tpt)
REVERT: C  166 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: C  246 PHE cc_start: 0.7576 (t80) cc_final: 0.7374 (t80)
REVERT: C  267 MET cc_start: 0.8676 (mtm) cc_final: 0.8289 (mtp)
REVERT: C  301 GLN cc_start: 0.7873 (pm20) cc_final: 0.6990 (tt0)
REVERT: C  321 TRP cc_start: 0.9070 (m100) cc_final: 0.8473 (m100)
REVERT: C  330 MET cc_start: 0.7428 (tpp) cc_final: 0.7081 (ttp)
REVERT: C  352 MET cc_start: 0.8712 (mmt) cc_final: 0.8268 (mmp)
REVERT: C  359 TYR cc_start: 0.7240 (m-10) cc_final: 0.6900 (m-80)
REVERT: A   18 MET cc_start: 0.8386 (tmm) cc_final: 0.7964 (tmm)
REVERT: A   37 LEU cc_start: 0.8448 (tp) cc_final: 0.8124 (tt)
REVERT: A  200 ASP cc_start: 0.7563 (t0) cc_final: 0.7049 (m-30)
REVERT: A  209 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8631 (ttpp)
REVERT: A  259 PHE cc_start: 0.8884 (m-80) cc_final: 0.8322 (m-80)
REVERT: A  265 ILE cc_start: 0.9067 (mt) cc_final: 0.8708 (mm)
REVERT: A  277 LYS cc_start: 0.7222 (tttt) cc_final: 0.6802 (tttt)
REVERT: B   57 LYS cc_start: 0.8679 (mttt) cc_final: 0.7812 (mtmt)
REVERT: B   75 GLN cc_start: 0.8581 (mp10) cc_final: 0.8030 (mp10)
REVERT: B   85 TYR cc_start: 0.8348 (m-80) cc_final: 0.8141 (m-80)
REVERT: B  201 SER cc_start: 0.7492 (p) cc_final: 0.7140 (p)
REVERT: B  246 ASP cc_start: 0.8704 (m-30) cc_final: 0.7997 (m-30)
REVERT: B  311 HIS cc_start: 0.7957 (m-70) cc_final: 0.7645 (m-70)
REVERT: G   38 GLU cc_start: 0.8992 (mp0) cc_final: 0.8421 (mm-30)
REVERT: G   41 ARG cc_start: 0.8789 (pmt-80) cc_final: 0.7825 (ttp80)
  outliers start: 1
  outliers final: 1
  residues processed: 225
  average time/residue: 0.1838
  time to fit residues: 57.1173
Evaluate side-chains
  172 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 71 optimal weight:    0.1980
   chunk 43 optimal weight:    4.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 ASN
A 188 HIS
A 195 HIS
** B 176 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.106212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.079629 restraints weight = 105516.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.082929 restraints weight = 36648.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.085434 restraints weight = 20301.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.6123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8063  Z= 0.284
  Angle     :  0.705   7.301  10926  Z= 0.375
  Chirality :  0.047   0.326   1252
  Planarity :  0.004   0.047   1384
  Dihedral  :  4.931  21.931   1092
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.27), residues: 992
  helix:  0.89 (0.24), residues: 459
  sheet: -0.29 (0.42), residues: 172
  loop : -1.30 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.015   0.002   PHE A 108 
 TYR   0.017   0.002   TYR B 124 
 ARG   0.009   0.001   ARG A  32 

*********************** 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
  201 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.8354 (tpt) cc_final: 0.7712 (tpt)
REVERT: C  166 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: C  267 MET cc_start: 0.8767 (mtm) cc_final: 0.8367 (mtp)
REVERT: C  293 MET cc_start: 0.6343 (pmm) cc_final: 0.5394 (ppp)
REVERT: C  321 TRP cc_start: 0.9032 (m100) cc_final: 0.8425 (m100)
REVERT: C  330 MET cc_start: 0.7582 (tpp) cc_final: 0.7108 (ttp)
REVERT: C  348 HIS cc_start: 0.8206 (m90) cc_final: 0.7823 (m90)
REVERT: C  352 MET cc_start: 0.8674 (mmt) cc_final: 0.8199 (mmp)
REVERT: C  359 TYR cc_start: 0.7403 (m-10) cc_final: 0.6769 (m-80)
REVERT: A   18 MET cc_start: 0.8424 (tmm) cc_final: 0.7952 (tmm)
REVERT: A  155 TYR cc_start: 0.8747 (m-80) cc_final: 0.8148 (m-80)
REVERT: A  209 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8660 (ttpt)
REVERT: A  248 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8050 (ptpp)
REVERT: A  259 PHE cc_start: 0.8912 (m-80) cc_final: 0.8264 (m-80)
REVERT: A  265 ILE cc_start: 0.9058 (mt) cc_final: 0.8657 (mm)
REVERT: A  347 ASN cc_start: 0.8746 (m-40) cc_final: 0.8499 (m110)
REVERT: B   57 LYS cc_start: 0.8859 (mttt) cc_final: 0.8215 (mtmt)
REVERT: B   75 GLN cc_start: 0.8654 (mp10) cc_final: 0.8083 (mp10)
REVERT: B   85 TYR cc_start: 0.8651 (m-80) cc_final: 0.8278 (m-80)
REVERT: B  201 SER cc_start: 0.7486 (p) cc_final: 0.7130 (p)
REVERT: G   38 GLU cc_start: 0.9035 (mp0) cc_final: 0.8474 (mp0)
REVERT: G   44 VAL cc_start: 0.9225 (m) cc_final: 0.8889 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1663
  time to fit residues: 48.1711
Evaluate side-chains
  159 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:   30.0000
   chunk 75 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 HIS
** B 176 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.109725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.083030 restraints weight = 94388.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.086779 restraints weight = 33844.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.089026 restraints weight = 18069.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3405
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3405 r_free = 0.3405    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3405 r_free = 0.3405    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3405
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.6332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8063  Z= 0.212
  Angle     :  0.669   7.346  10926  Z= 0.354
  Chirality :  0.046   0.299   1252
  Planarity :  0.004   0.047   1384
  Dihedral  :  4.743  20.307   1092
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.28), residues: 992
  helix:  0.99 (0.24), residues: 461
  sheet: -0.27 (0.41), residues: 179
  loop : -1.21 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B  82 
 HIS   0.008   0.001   HIS B 142 
 PHE   0.022   0.002   PHE B 241 
 TYR   0.016   0.001   TYR B 124 
 ARG   0.007   0.001   ARG A  32 

*********************** 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
  208 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.8291 (tpt) cc_final: 0.7751 (tpt)
REVERT: C  267 MET cc_start: 0.8666 (mtm) cc_final: 0.8351 (mtp)
REVERT: C  293 MET cc_start: 0.6240 (pmm) cc_final: 0.5158 (ppp)
REVERT: C  301 GLN cc_start: 0.8041 (pm20) cc_final: 0.7242 (tt0)
REVERT: C  320 CYS cc_start: 0.7606 (m) cc_final: 0.7384 (m)
REVERT: C  321 TRP cc_start: 0.9037 (m100) cc_final: 0.8725 (m100)
REVERT: C  330 MET cc_start: 0.7383 (tpp) cc_final: 0.6928 (ttp)
REVERT: C  348 HIS cc_start: 0.8315 (m90) cc_final: 0.7937 (m90)
REVERT: C  352 MET cc_start: 0.8714 (mmt) cc_final: 0.8319 (mmp)
REVERT: C  359 TYR cc_start: 0.7300 (m-10) cc_final: 0.6810 (m-80)
REVERT: A   18 MET cc_start: 0.8390 (tmm) cc_final: 0.7955 (tmm)
REVERT: A   28 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8574 (mm-30)
REVERT: A  155 TYR cc_start: 0.8753 (m-80) cc_final: 0.8186 (m-80)
REVERT: A  200 ASP cc_start: 0.7746 (t0) cc_final: 0.7528 (t0)
REVERT: A  209 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8634 (ttpt)
REVERT: A  259 PHE cc_start: 0.8863 (m-80) cc_final: 0.8282 (m-80)
REVERT: A  265 ILE cc_start: 0.9125 (mt) cc_final: 0.8758 (mm)
REVERT: A  277 LYS cc_start: 0.7397 (tttt) cc_final: 0.7047 (tttt)
REVERT: B   85 TYR cc_start: 0.8599 (m-80) cc_final: 0.8323 (m-80)
REVERT: B  246 ASP cc_start: 0.8588 (m-30) cc_final: 0.7977 (m-30)
REVERT: B  261 LEU cc_start: 0.9138 (tt) cc_final: 0.8900 (tt)
REVERT: B  311 HIS cc_start: 0.7816 (m-70) cc_final: 0.7532 (m-70)
REVERT: G   35 LYS cc_start: 0.9278 (pptt) cc_final: 0.8849 (ttpt)
REVERT: G   38 GLU cc_start: 0.9007 (mp0) cc_final: 0.8074 (mp0)
REVERT: G   41 ARG cc_start: 0.8783 (pmt-80) cc_final: 0.7718 (ttp80)
REVERT: G   47 ARG cc_start: 0.8332 (mmt180) cc_final: 0.7867 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1839
  time to fit residues: 53.9758
Evaluate side-chains
  165 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.106058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.076456 restraints weight = 92057.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080676 restraints weight = 35013.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.083588 restraints weight = 19018.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.6528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8063  Z= 0.272
  Angle     :  0.713   7.251  10926  Z= 0.375
  Chirality :  0.047   0.280   1252
  Planarity :  0.004   0.049   1384
  Dihedral  :  4.938  20.891   1092
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.27), residues: 992
  helix:  0.90 (0.24), residues: 459
  sheet: -0.56 (0.39), residues: 188
  loop : -1.11 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP B 339 
 HIS   0.008   0.001   HIS A 195 
 PHE   0.020   0.002   PHE B 278 
 TYR   0.013   0.002   TYR C  62 
 ARG   0.007   0.001   ARG A  32 

*********************** 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
  205 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.8395 (tpt) cc_final: 0.7775 (tpt)
REVERT: C  267 MET cc_start: 0.8557 (mtm) cc_final: 0.8350 (mtp)
REVERT: C  293 MET cc_start: 0.6233 (pmm) cc_final: 0.5256 (ppp)
REVERT: C  321 TRP cc_start: 0.9048 (m100) cc_final: 0.8660 (m100)
REVERT: C  330 MET cc_start: 0.7536 (tpp) cc_final: 0.7021 (ttp)
REVERT: C  348 HIS cc_start: 0.8080 (m90) cc_final: 0.7799 (m90)
REVERT: C  352 MET cc_start: 0.8610 (mmt) cc_final: 0.8145 (mmp)
REVERT: C  359 TYR cc_start: 0.7362 (m-10) cc_final: 0.6671 (m-80)
REVERT: A   18 MET cc_start: 0.8390 (tmm) cc_final: 0.7934 (tmm)
REVERT: A   28 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8586 (mm-30)
REVERT: A  155 TYR cc_start: 0.8763 (m-80) cc_final: 0.7988 (m-80)
REVERT: A  209 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8673 (ttpp)
REVERT: A  248 LYS cc_start: 0.8311 (ptpp) cc_final: 0.7937 (ptpp)
REVERT: A  251 ASP cc_start: 0.8334 (t0) cc_final: 0.7827 (t0)
REVERT: A  259 PHE cc_start: 0.8987 (m-80) cc_final: 0.8388 (m-80)
REVERT: A  277 LYS cc_start: 0.7468 (tttt) cc_final: 0.7152 (tttt)
REVERT: B   75 GLN cc_start: 0.8917 (mp10) cc_final: 0.8236 (mp10)
REVERT: B   85 TYR cc_start: 0.8829 (m-80) cc_final: 0.8434 (m-80)
REVERT: B  233 CYS cc_start: 0.7477 (p) cc_final: 0.6843 (p)
REVERT: B  246 ASP cc_start: 0.8350 (m-30) cc_final: 0.7844 (m-30)
REVERT: B  261 LEU cc_start: 0.9175 (tt) cc_final: 0.8913 (tt)
REVERT: G   38 GLU cc_start: 0.8931 (mp0) cc_final: 0.8326 (mm-30)
REVERT: G   41 ARG cc_start: 0.8815 (pmt-80) cc_final: 0.7836 (ttp80)
REVERT: G   47 ARG cc_start: 0.8174 (mmt180) cc_final: 0.7960 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2697
  time to fit residues: 77.3332
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  : 2.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    0.2980
   chunk 60 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 89 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
C 270 GLN
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.110186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.083265 restraints weight = 113308.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.088000 restraints weight = 41187.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.090005 restraints weight = 20816.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    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 = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.6639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8063  Z= 0.196
  Angle     :  0.687   7.965  10926  Z= 0.359
  Chirality :  0.045   0.257   1252
  Planarity :  0.004   0.054   1384
  Dihedral  :  4.812  23.112   1092
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.27), residues: 992
  helix:  1.03 (0.24), residues: 456
  sheet: -0.48 (0.38), residues: 185
  loop : -1.09 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP B 339 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.023   0.002   PHE B 241 
 TYR   0.011   0.001   TYR C 333 
 ARG   0.008   0.001   ARG C 328 

********************** 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
  215 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.8311 (tpt) cc_final: 0.7872 (tpt)
REVERT: C  293 MET cc_start: 0.6197 (pmm) cc_final: 0.5238 (ppp)
REVERT: C  301 GLN cc_start: 0.8086 (pm20) cc_final: 0.7329 (tt0)
REVERT: C  321 TRP cc_start: 0.9072 (m100) cc_final: 0.8506 (m100)
REVERT: C  330 MET cc_start: 0.7331 (tpp) cc_final: 0.6911 (ttp)
REVERT: C  348 HIS cc_start: 0.8163 (m90) cc_final: 0.7870 (m90)
REVERT: C  352 MET cc_start: 0.8633 (mmt) cc_final: 0.8231 (mmt)
REVERT: C  359 TYR cc_start: 0.7133 (m-10) cc_final: 0.6887 (m-80)
REVERT: A   18 MET cc_start: 0.8214 (tmm) cc_final: 0.7431 (tmm)
REVERT: A   28 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8595 (mm-30)
REVERT: A   52 GLN cc_start: 0.8692 (pt0) cc_final: 0.8348 (pt0)
REVERT: A  155 TYR cc_start: 0.8378 (m-80) cc_final: 0.7832 (m-80)
REVERT: A  200 ASP cc_start: 0.7741 (t0) cc_final: 0.7485 (t0)
REVERT: A  209 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8565 (ttpp)
REVERT: A  259 PHE cc_start: 0.8800 (m-80) cc_final: 0.8246 (m-80)
REVERT: A  265 ILE cc_start: 0.9034 (mt) cc_final: 0.8822 (mm)
REVERT: A  277 LYS cc_start: 0.7466 (tttt) cc_final: 0.7186 (tttt)
REVERT: A  347 ASN cc_start: 0.8838 (m-40) cc_final: 0.8596 (m110)
REVERT: B   57 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8026 (mtmt)
REVERT: B   85 TYR cc_start: 0.8668 (m-80) cc_final: 0.8341 (m-80)
REVERT: B  190 LEU cc_start: 0.8981 (tt) cc_final: 0.8756 (tt)
REVERT: B  246 ASP cc_start: 0.8370 (m-30) cc_final: 0.7867 (m-30)
REVERT: B  311 HIS cc_start: 0.7931 (m-70) cc_final: 0.7607 (m90)
REVERT: G   38 GLU cc_start: 0.8893 (mp0) cc_final: 0.8305 (mm-30)
REVERT: G   41 ARG cc_start: 0.8804 (pmt-80) cc_final: 0.7179 (ttp80)
REVERT: G   45 GLU cc_start: 0.8659 (mp0) cc_final: 0.8366 (mp0)
REVERT: G   47 ARG cc_start: 0.8259 (mmt180) cc_final: 0.7841 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1879
  time to fit residues: 56.0402
Evaluate side-chains
  162 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 60 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0870
   chunk 41 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.109395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.082741 restraints weight = 86842.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.087182 restraints weight = 32570.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.089747 restraints weight = 17413.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.6726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8063  Z= 0.227
  Angle     :  0.723  10.519  10926  Z= 0.377
  Chirality :  0.047   0.323   1252
  Planarity :  0.004   0.049   1384
  Dihedral  :  4.793  22.657   1092
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.27), residues: 992
  helix:  1.08 (0.24), residues: 456
  sheet: -0.37 (0.39), residues: 177
  loop : -1.18 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP B 339 
 HIS   0.008   0.001   HIS A 195 
 PHE   0.031   0.002   PHE A 108 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.008   0.001   ARG C 149 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3640.94 seconds
wall clock time: 66 minutes 34.45 seconds (3994.45 seconds total)