Starting phenix.real_space_refine
on Wed Feb 12 00:26:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0r_23101/02_2025/7l0r_23101.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0r_23101/02_2025/7l0r_23101.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l0r_23101/02_2025/7l0r_23101.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0r_23101/02_2025/7l0r_23101.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0r_23101/02_2025/7l0r_23101.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0r_23101/02_2025/7l0r_23101.cif"
  }
  resolution = 4.2
  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      53      5.16       5
     C    4450      2.51       5
     N    1176      2.21       5
     O    1289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6968
  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: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1791
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 2
    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}
  Time building chain proxies: 4.71, per 1000 atoms: 0.68
  Number of scatterers: 6968
  At special positions: 0
  Unit cell: (75.075, 112.2, 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      53     16.00
     O    1289      8.00
     N    1176      7.00
     C    4450      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: 1.79
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1666

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      43.9% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  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: 3.508A  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 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: 5.048A  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: 4.405A  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: 7.784A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.292A  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: 7.232A  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: 6.534A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.321A  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: 7.603A  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: 8.202A  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: 4.245A  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: 6.848A  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: 4.346A  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: 4.396A  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: 5.142A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.736A  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: 6.063A  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)

    364 hydrogen bonds defined for protein.
    1062 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: 2.17

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1875
        1.33 -     1.45: 1457
        1.45 -     1.57: 3699
        1.57 -     1.69: 0
        1.69 -     1.81: 77
  Bond restraints: 7108
  Sorted by residual:
  bond pdb=" C   HIS C 133 "
       pdb=" N   PRO C 134 "
    ideal  model  delta    sigma   weight residual
    1.331  1.385 -0.053 1.28e-02 6.10e+03 1.72e+01
  bond pdb=" N   LEU B  95 "
       pdb=" CA  LEU B  95 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.17e-02 7.31e+03 8.30e+00
  bond pdb=" N   ASP A 309 "
       pdb=" CA  ASP A 309 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.33e-02 5.65e+03 6.36e+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 6.14e+00
  bond pdb=" N   ASP B 323 "
       pdb=" CA  ASP B 323 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.31e-02 5.83e+03 5.83e+00
  ... (remaining 7103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 8677
        2.06 -     4.13: 764
        4.13 -     6.19: 132
        6.19 -     8.26: 38
        8.26 -    10.32: 20
  Bond angle restraints: 9631
  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   99.00    8.51 1.49e+00 4.50e-01 3.26e+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  105.13    6.15 1.09e+00 8.42e-01 3.18e+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  127.90   -7.08 1.47e+00 4.63e-01 2.32e+01
  angle pdb=" C   CYS A   3 "
        pdb=" N   THR A   4 "
        pdb=" CA  THR A   4 "
      ideal   model   delta    sigma   weight residual
     121.54  130.72   -9.18 1.91e+00 2.74e-01 2.31e+01
  ... (remaining 9626 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 3770
       15.98 -    31.96: 329
       31.96 -    47.93: 77
       47.93 -    63.91: 24
       63.91 -    79.89: 4
  Dihedral angle restraints: 4204
    sinusoidal: 1628
      harmonic: 2576
  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 -165.89   79.89     1      1.00e+01 1.00e-02 7.91e+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  153.89   26.11     0      5.00e+00 4.00e-02 2.73e+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  156.29   23.71     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 4201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 836
       0.082 -    0.164: 221
       0.164 -    0.246: 41
       0.246 -    0.328: 13
       0.328 -    0.410: 1
  Chirality restraints: 1112
  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 4.20e+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 2.20e+00
  ... (remaining 1109 not shown)

  Planarity restraints: 1209
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 374 "    0.027 2.00e-02 2.50e+03   5.30e-02 2.81e+01
        pdb=" C   ALA C 374 "   -0.092 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   3.35e-02 1.12e+01
        pdb=" C   ARG B  49 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ARG B  49 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR B  50 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 300 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.01e+01
        pdb=" C   VAL C 300 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL C 300 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN C 301 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1206 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 201
        2.66 -     3.22: 6562
        3.22 -     3.78: 11590
        3.78 -     4.34: 14908
        4.34 -     4.90: 24418
  Nonbonded interactions: 57679
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 146 "
            pdb=" OXT LEU D  13 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.232 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
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.304 3.040
  ... (remaining 57674 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.890
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
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      :  0.007   0.081   7108  Z= 0.479
  Angle     :  1.372  10.325   9631  Z= 0.787
  Chirality :  0.079   0.410   1112
  Planarity :  0.008   0.058   1209
  Dihedral  : 13.578  70.468   2535
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.26 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.24 %
  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: -3.44 (0.24), residues: 869
  helix: -1.98 (0.20), residues: 376
  sheet: -2.25 (0.36), residues: 173
  loop : -2.41 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.004   TRP B 297 
 HIS   0.008   0.003   HIS A 188 
 PHE   0.038   0.004   PHE C 376 
 TYR   0.029   0.004   TYR C 349 
 ARG   0.012   0.001   ARG B 314 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 301
  time to evaluate  : 0.732 
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  169 LEU cc_start: 0.8671 (tp) cc_final: 0.8437 (tp)
REVERT: C  305 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8325 (mtt-85)
REVERT: A   21 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7589 (tpp80)
REVERT: A   22 ASN cc_start: 0.8967 (m-40) cc_final: 0.8759 (m110)
REVERT: A   28 GLU cc_start: 0.8303 (tt0) cc_final: 0.7854 (tm-30)
REVERT: A  321 THR cc_start: 0.7498 (p) cc_final: 0.7253 (p)
REVERT: B   46 ARG cc_start: 0.6912 (tpt-90) cc_final: 0.6697 (mtp-110)
REVERT: B   51 LEU cc_start: 0.8445 (mp) cc_final: 0.8086 (mp)
REVERT: B   79 LEU cc_start: 0.9142 (pt) cc_final: 0.8914 (pp)
REVERT: B   82 TRP cc_start: 0.8585 (m100) cc_final: 0.8375 (m100)
REVERT: B   93 ILE cc_start: 0.9144 (mt) cc_final: 0.8895 (mt)
REVERT: B   99 TRP cc_start: 0.8466 (m100) cc_final: 0.8052 (m100)
REVERT: B  126 LEU cc_start: 0.8266 (mp) cc_final: 0.8017 (mp)
REVERT: B  149 CYS cc_start: 0.8130 (p) cc_final: 0.7716 (m)
REVERT: B  188 MET cc_start: 0.8407 (mmm) cc_final: 0.8064 (mmm)
REVERT: B  308 LEU cc_start: 0.8750 (tp) cc_final: 0.7640 (tp)
REVERT: B  312 ASP cc_start: 0.7384 (p0) cc_final: 0.6928 (t0)
REVERT: B  329 THR cc_start: 0.9075 (t) cc_final: 0.8805 (t)
  outliers start: 8
  outliers final: 3
  residues processed: 306
  average time/residue: 0.2700
  time to fit residues: 103.1305
Evaluate side-chains
  206 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 203
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN
C 159 ASN
C 219 HIS
C 239 GLN
C 292 ASN
A 188 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 295 ASN
B 311 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.112370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.091627 restraints weight = 21102.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094189 restraints weight = 13056.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.095955 restraints weight = 9240.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7108  Z= 0.190
  Angle     :  0.707   8.937   9631  Z= 0.374
  Chirality :  0.046   0.217   1112
  Planarity :  0.005   0.040   1209
  Dihedral  :  5.739  59.180    955
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.25), residues: 869
  helix: -0.38 (0.23), residues: 380
  sheet: -1.45 (0.36), residues: 174
  loop : -2.42 (0.30), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 339 
 HIS   0.011   0.002   HIS C 325 
 PHE   0.043   0.002   PHE C 246 
 TYR   0.021   0.002   TYR C 369 
 ARG   0.008   0.001   ARG B  42 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 272
  time to evaluate  : 0.879 
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  167 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.8174 (mtp85)
REVERT: C  169 LEU cc_start: 0.8933 (tp) cc_final: 0.8714 (tp)
REVERT: C  234 LEU cc_start: 0.9202 (tt) cc_final: 0.8852 (mt)
REVERT: C  345 ASP cc_start: 0.8384 (m-30) cc_final: 0.7813 (m-30)
REVERT: C  346 PHE cc_start: 0.8798 (t80) cc_final: 0.8452 (t80)
REVERT: C  357 LEU cc_start: 0.9366 (mt) cc_final: 0.9072 (mt)
REVERT: A   28 GLU cc_start: 0.8146 (tt0) cc_final: 0.7895 (tm-30)
REVERT: A  204 GLN cc_start: 0.7786 (pp30) cc_final: 0.7428 (pp30)
REVERT: A  243 MET cc_start: 0.8337 (tpp) cc_final: 0.7869 (tpp)
REVERT: A  343 ILE cc_start: 0.9252 (tp) cc_final: 0.9022 (tp)
REVERT: B   59 TYR cc_start: 0.8393 (m-80) cc_final: 0.7921 (m-80)
REVERT: B   61 MET cc_start: 0.7835 (ppp) cc_final: 0.7553 (ppp)
REVERT: B  149 CYS cc_start: 0.8085 (p) cc_final: 0.7725 (m)
REVERT: B  212 ASP cc_start: 0.5665 (t0) cc_final: 0.4699 (t0)
REVERT: B  261 LEU cc_start: 0.8818 (tt) cc_final: 0.8525 (tt)
REVERT: B  325 MET cc_start: 0.8537 (mmm) cc_final: 0.8336 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 273
  average time/residue: 0.2340
  time to fit residues: 83.6077
Evaluate side-chains
  196 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
C 132 HIS
C 159 ASN
C 239 GLN
C 270 GLN
C 355 ASN
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 230 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.110788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.090138 restraints weight = 21757.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.092668 restraints weight = 13256.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.094413 restraints weight = 9372.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7108  Z= 0.220
  Angle     :  0.679   7.405   9631  Z= 0.361
  Chirality :  0.045   0.181   1112
  Planarity :  0.004   0.050   1209
  Dihedral  :  5.419  61.372    955
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.71 %
    Favored  : 95.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.27), residues: 869
  helix:  0.37 (0.26), residues: 377
  sheet: -1.40 (0.35), residues: 180
  loop : -2.16 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.008   0.001   HIS B 311 
 PHE   0.022   0.002   PHE C 376 
 TYR   0.017   0.002   TYR C 105 
 ARG   0.005   0.001   ARG B  52 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 251
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  234 LEU cc_start: 0.9186 (tt) cc_final: 0.8830 (mt)
REVERT: C  250 MET cc_start: 0.8083 (ptm) cc_final: 0.7848 (ptm)
REVERT: C  345 ASP cc_start: 0.8375 (m-30) cc_final: 0.7804 (m-30)
REVERT: C  346 PHE cc_start: 0.8744 (t80) cc_final: 0.8495 (t80)
REVERT: C  357 LEU cc_start: 0.9354 (mt) cc_final: 0.9074 (mt)
REVERT: A   18 MET cc_start: 0.8433 (tpp) cc_final: 0.8029 (tpp)
REVERT: A   21 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8219 (ttm170)
REVERT: A   28 GLU cc_start: 0.8069 (tt0) cc_final: 0.7824 (tm-30)
REVERT: A  333 GLN cc_start: 0.7962 (pm20) cc_final: 0.7702 (pm20)
REVERT: B  118 ASP cc_start: 0.8237 (p0) cc_final: 0.7853 (p0)
REVERT: B  146 LEU cc_start: 0.9155 (mp) cc_final: 0.8949 (mt)
REVERT: B  149 CYS cc_start: 0.8242 (p) cc_final: 0.7851 (m)
REVERT: G   41 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7896 (ttp80)
REVERT: G   42 ASP cc_start: 0.8605 (p0) cc_final: 0.7762 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2105
  time to fit residues: 67.7072
Evaluate side-chains
  191 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.0000
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 78 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
C 270 GLN
C 325 HIS
A 195 HIS
B  88 ASN
B 230 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.111104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.090369 restraints weight = 21444.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.093115 restraints weight = 12549.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094985 restraints weight = 8570.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7108  Z= 0.201
  Angle     :  0.649   7.077   9631  Z= 0.344
  Chirality :  0.044   0.148   1112
  Planarity :  0.004   0.053   1209
  Dihedral  :  5.317  58.448    955
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.40 %
    Favored  : 96.47 %
  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: -0.99 (0.28), residues: 869
  helix:  0.70 (0.26), residues: 377
  sheet: -0.99 (0.36), residues: 185
  loop : -2.12 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.024   0.002   PHE A 307 
 TYR   0.016   0.002   TYR C 349 
 ARG   0.008   0.001   ARG A 208 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  161 VAL cc_start: 0.8943 (t) cc_final: 0.8645 (p)
REVERT: C  166 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: C  234 LEU cc_start: 0.9208 (tt) cc_final: 0.8856 (mt)
REVERT: C  250 MET cc_start: 0.8102 (ptm) cc_final: 0.7817 (ptm)
REVERT: C  345 ASP cc_start: 0.8481 (m-30) cc_final: 0.7877 (m-30)
REVERT: C  346 PHE cc_start: 0.8820 (t80) cc_final: 0.8572 (t80)
REVERT: A   21 ARG cc_start: 0.8731 (ttm170) cc_final: 0.8464 (ttm170)
REVERT: A   22 ASN cc_start: 0.9070 (m110) cc_final: 0.8573 (m110)
REVERT: A   28 GLU cc_start: 0.8097 (tt0) cc_final: 0.7769 (tm-30)
REVERT: A  197 LYS cc_start: 0.7684 (mptt) cc_final: 0.7470 (mmtt)
REVERT: A  204 GLN cc_start: 0.7888 (pp30) cc_final: 0.7472 (pp30)
REVERT: A  209 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8273 (ttpp)
REVERT: A  333 GLN cc_start: 0.8095 (pm20) cc_final: 0.7867 (pm20)
REVERT: B   45 MET cc_start: 0.7910 (mmp) cc_final: 0.7102 (tpp)
REVERT: B  118 ASP cc_start: 0.8282 (p0) cc_final: 0.7958 (p0)
REVERT: B  146 LEU cc_start: 0.9043 (mp) cc_final: 0.8749 (mt)
REVERT: B  149 CYS cc_start: 0.8307 (p) cc_final: 0.7884 (m)
REVERT: B  225 HIS cc_start: 0.5549 (m-70) cc_final: 0.4987 (m-70)
REVERT: B  289 TYR cc_start: 0.8108 (m-80) cc_final: 0.7845 (m-80)
REVERT: G   38 GLU cc_start: 0.8408 (tp30) cc_final: 0.6908 (tp30)
REVERT: G   41 ARG cc_start: 0.8383 (tmm160) cc_final: 0.8011 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2006
  time to fit residues: 64.1430
Evaluate side-chains
  184 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0970
   chunk 81 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
C 159 ASN
C 325 HIS
A 306 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 230 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.112772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.093324 restraints weight = 20797.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.095783 restraints weight = 12849.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.097515 restraints weight = 9031.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.4972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7108  Z= 0.202
  Angle     :  0.656   7.248   9631  Z= 0.342
  Chirality :  0.044   0.162   1112
  Planarity :  0.004   0.051   1209
  Dihedral  :  5.140  55.639    955
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.14 %
    Favored  : 96.60 %
  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: -0.75 (0.28), residues: 869
  helix:  0.86 (0.26), residues: 378
  sheet: -0.78 (0.37), residues: 180
  loop : -2.00 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.021   0.002   PHE C 344 
 TYR   0.018   0.002   TYR B  59 
 ARG   0.009   0.001   ARG A 208 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 231
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  234 LEU cc_start: 0.9146 (tt) cc_final: 0.8801 (mt)
REVERT: C  250 MET cc_start: 0.8127 (ptm) cc_final: 0.7762 (ptm)
REVERT: C  345 ASP cc_start: 0.8443 (m-30) cc_final: 0.7766 (m-30)
REVERT: C  346 PHE cc_start: 0.8681 (t80) cc_final: 0.8363 (t80)
REVERT: C  357 LEU cc_start: 0.9309 (mt) cc_final: 0.9069 (mt)
REVERT: A   21 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8360 (ttm170)
REVERT: A  197 LYS cc_start: 0.7805 (mptt) cc_final: 0.7599 (mmtt)
REVERT: A  209 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8185 (ttpp)
REVERT: A  343 ILE cc_start: 0.9278 (tp) cc_final: 0.8871 (tp)
REVERT: A  347 ASN cc_start: 0.8396 (m110) cc_final: 0.8021 (m110)
REVERT: B   45 MET cc_start: 0.7746 (mmp) cc_final: 0.7112 (mmt)
REVERT: B   59 TYR cc_start: 0.8397 (m-10) cc_final: 0.8133 (m-80)
REVERT: B  118 ASP cc_start: 0.8277 (p0) cc_final: 0.8005 (p0)
REVERT: B  146 LEU cc_start: 0.9162 (mp) cc_final: 0.8953 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1948
  time to fit residues: 59.4719
Evaluate side-chains
  173 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 16 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS
** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 230 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.111082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.090672 restraints weight = 21446.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.093103 restraints weight = 13208.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.094818 restraints weight = 9426.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.5282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7108  Z= 0.229
  Angle     :  0.687   8.026   9631  Z= 0.359
  Chirality :  0.045   0.168   1112
  Planarity :  0.005   0.069   1209
  Dihedral  :  5.208  54.583    955
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.14 %
    Favored  : 96.73 %
  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: -0.51 (0.29), residues: 869
  helix:  1.05 (0.27), residues: 373
  sheet: -0.77 (0.37), residues: 189
  loop : -1.74 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B 297 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.042   0.002   PHE C 344 
 TYR   0.018   0.002   TYR C 349 
 ARG   0.011   0.001   ARG A 208 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.6768 (m-40) cc_final: 0.6510 (m-40)
REVERT: C  153 THR cc_start: 0.8159 (p) cc_final: 0.7890 (t)
REVERT: C  161 VAL cc_start: 0.8910 (t) cc_final: 0.8580 (p)
REVERT: C  166 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7516 (tm-30)
REVERT: C  234 LEU cc_start: 0.9153 (tt) cc_final: 0.8823 (mt)
REVERT: C  250 MET cc_start: 0.8113 (ptm) cc_final: 0.7679 (ptm)
REVERT: C  345 ASP cc_start: 0.8506 (m-30) cc_final: 0.7971 (m-30)
REVERT: C  346 PHE cc_start: 0.8764 (t80) cc_final: 0.8428 (t80)
REVERT: C  357 LEU cc_start: 0.9336 (mt) cc_final: 0.9117 (mt)
REVERT: C  364 ILE cc_start: 0.8310 (tt) cc_final: 0.8086 (tp)
REVERT: A   21 ARG cc_start: 0.8673 (ttm170) cc_final: 0.8464 (ttm170)
REVERT: A   22 ASN cc_start: 0.8916 (m110) cc_final: 0.8371 (m110)
REVERT: A   37 LEU cc_start: 0.9088 (tp) cc_final: 0.8829 (tt)
REVERT: A  197 LYS cc_start: 0.7803 (mptt) cc_final: 0.7582 (mmtt)
REVERT: A  209 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8108 (ttpp)
REVERT: A  240 MET cc_start: 0.4005 (pmm) cc_final: 0.3669 (pmm)
REVERT: B   45 MET cc_start: 0.7820 (mmp) cc_final: 0.7276 (mmm)
REVERT: B  225 HIS cc_start: 0.5502 (m-70) cc_final: 0.4815 (m-70)
REVERT: B  251 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7408 (mpt-90)
REVERT: G   31 MET cc_start: 0.3318 (mtt) cc_final: 0.3010 (mtp)
REVERT: G   37 CYS cc_start: 0.8436 (m) cc_final: 0.8099 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1929
  time to fit residues: 58.0007
Evaluate side-chains
  166 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 58 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
C 127 ASN
C 325 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.112461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.092476 restraints weight = 21044.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.094924 restraints weight = 13010.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.096601 restraints weight = 9199.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.5561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7108  Z= 0.205
  Angle     :  0.683   7.929   9631  Z= 0.357
  Chirality :  0.046   0.140   1112
  Planarity :  0.005   0.054   1209
  Dihedral  :  5.278  63.430    955
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.83 %
    Favored  : 98.04 %
  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: -0.56 (0.29), residues: 869
  helix:  0.96 (0.26), residues: 379
  sheet: -0.83 (0.37), residues: 183
  loop : -1.72 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.022   0.002   PHE C 344 
 TYR   0.015   0.002   TYR C 333 
 ARG   0.012   0.001   ARG A 205 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.6812 (m-40) cc_final: 0.6600 (m-40)
REVERT: C  161 VAL cc_start: 0.8888 (t) cc_final: 0.8535 (p)
REVERT: C  234 LEU cc_start: 0.9150 (tt) cc_final: 0.8810 (mt)
REVERT: C  250 MET cc_start: 0.8119 (ptm) cc_final: 0.7686 (ptm)
REVERT: C  305 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8412 (mtt-85)
REVERT: C  321 TRP cc_start: 0.8546 (m100) cc_final: 0.8305 (m100)
REVERT: C  344 PHE cc_start: 0.8030 (t80) cc_final: 0.7131 (t80)
REVERT: C  345 ASP cc_start: 0.8478 (m-30) cc_final: 0.7301 (p0)
REVERT: C  346 PHE cc_start: 0.8684 (t80) cc_final: 0.8266 (t80)
REVERT: C  357 LEU cc_start: 0.9337 (mt) cc_final: 0.9117 (mt)
REVERT: C  364 ILE cc_start: 0.8233 (tt) cc_final: 0.7970 (tp)
REVERT: A  209 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8071 (ttpp)
REVERT: A  240 MET cc_start: 0.4110 (pmm) cc_final: 0.3755 (pmm)
REVERT: A  254 CYS cc_start: 0.8267 (p) cc_final: 0.8065 (p)
REVERT: A  333 GLN cc_start: 0.7799 (pm20) cc_final: 0.7444 (pm20)
REVERT: B   45 MET cc_start: 0.7800 (mmp) cc_final: 0.7272 (tpp)
REVERT: B  118 ASP cc_start: 0.8425 (p0) cc_final: 0.8163 (p0)
REVERT: B  123 ILE cc_start: 0.9113 (mm) cc_final: 0.8586 (pt)
REVERT: B  129 ARG cc_start: 0.8441 (ppt170) cc_final: 0.8176 (ttp80)
REVERT: B  190 LEU cc_start: 0.9028 (tt) cc_final: 0.8692 (tt)
REVERT: G   31 MET cc_start: 0.3400 (mtt) cc_final: 0.2499 (ptp)
REVERT: G   37 CYS cc_start: 0.8305 (m) cc_final: 0.7975 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2201
  time to fit residues: 67.8498
Evaluate side-chains
  181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS
** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.110596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.090215 restraints weight = 21507.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.092593 restraints weight = 13253.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094290 restraints weight = 9443.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.5835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7108  Z= 0.223
  Angle     :  0.706   8.227   9631  Z= 0.368
  Chirality :  0.045   0.191   1112
  Planarity :  0.006   0.088   1209
  Dihedral  :  5.383  69.551    955
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.18 %
    Favored  : 98.69 %
  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: -0.42 (0.29), residues: 869
  helix:  1.03 (0.26), residues: 378
  sheet: -0.70 (0.38), residues: 177
  loop : -1.61 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 321 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.034   0.002   PHE C 344 
 TYR   0.032   0.002   TYR C 324 
 ARG   0.013   0.001   ARG A 205 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  161 VAL cc_start: 0.8886 (t) cc_final: 0.8538 (p)
REVERT: C  234 LEU cc_start: 0.9116 (tt) cc_final: 0.8816 (mt)
REVERT: C  238 ILE cc_start: 0.7316 (tt) cc_final: 0.7051 (tt)
REVERT: C  250 MET cc_start: 0.8127 (ptm) cc_final: 0.7708 (ptm)
REVERT: C  344 PHE cc_start: 0.7884 (t80) cc_final: 0.7124 (t80)
REVERT: C  345 ASP cc_start: 0.8471 (m-30) cc_final: 0.7193 (p0)
REVERT: C  346 PHE cc_start: 0.8692 (t80) cc_final: 0.8249 (t80)
REVERT: C  348 HIS cc_start: 0.8159 (m170) cc_final: 0.7957 (m170)
REVERT: C  357 LEU cc_start: 0.9338 (mt) cc_final: 0.9104 (mt)
REVERT: C  364 ILE cc_start: 0.8123 (tt) cc_final: 0.7844 (tp)
REVERT: A  209 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8001 (ttpp)
REVERT: A  240 MET cc_start: 0.4153 (pmm) cc_final: 0.3804 (pmm)
REVERT: B   45 MET cc_start: 0.7780 (mmp) cc_final: 0.7290 (tpp)
REVERT: B  118 ASP cc_start: 0.8473 (p0) cc_final: 0.8118 (p0)
REVERT: B  146 LEU cc_start: 0.9183 (mp) cc_final: 0.8330 (mp)
REVERT: B  190 LEU cc_start: 0.9055 (tt) cc_final: 0.8681 (tt)
REVERT: B  251 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7712 (mpt-90)
REVERT: G   31 MET cc_start: 0.3655 (mtt) cc_final: 0.3229 (mtp)
REVERT: G   41 ARG cc_start: 0.8431 (tmt170) cc_final: 0.8127 (tmt-80)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2001
  time to fit residues: 61.7066
Evaluate side-chains
  168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 68 optimal weight:    0.3980
   chunk 72 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0970
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS
** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
B 142 HIS
B 230 ASN
** B 295 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.113880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.093572 restraints weight = 21280.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.096068 restraints weight = 12965.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.097825 restraints weight = 9045.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.6066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7108  Z= 0.189
  Angle     :  0.719   8.665   9631  Z= 0.370
  Chirality :  0.046   0.224   1112
  Planarity :  0.005   0.063   1209
  Dihedral  :  5.325  68.679    955
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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: -0.43 (0.29), residues: 869
  helix:  1.05 (0.26), residues: 376
  sheet: -0.60 (0.39), residues: 175
  loop : -1.70 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.032   0.002   PHE C 344 
 TYR   0.021   0.002   TYR C 324 
 ARG   0.013   0.001   ARG A 205 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  161 VAL cc_start: 0.8877 (t) cc_final: 0.8514 (p)
REVERT: C  234 LEU cc_start: 0.9027 (tt) cc_final: 0.8779 (mt)
REVERT: C  238 ILE cc_start: 0.7221 (tt) cc_final: 0.6942 (tt)
REVERT: C  250 MET cc_start: 0.8116 (ptm) cc_final: 0.7739 (ptm)
REVERT: C  301 GLN cc_start: 0.8206 (pm20) cc_final: 0.7913 (pm20)
REVERT: C  345 ASP cc_start: 0.8379 (m-30) cc_final: 0.7947 (p0)
REVERT: C  346 PHE cc_start: 0.8660 (t80) cc_final: 0.8299 (t80)
REVERT: C  357 LEU cc_start: 0.9334 (mt) cc_final: 0.9107 (mt)
REVERT: A   22 ASN cc_start: 0.8876 (m110) cc_final: 0.8668 (m110)
REVERT: A  201 VAL cc_start: 0.8925 (t) cc_final: 0.8711 (t)
REVERT: A  209 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7965 (ttpp)
REVERT: B   45 MET cc_start: 0.7814 (mmp) cc_final: 0.7170 (tpp)
REVERT: B  123 ILE cc_start: 0.9032 (mm) cc_final: 0.8507 (pt)
REVERT: B  190 LEU cc_start: 0.9129 (tt) cc_final: 0.8813 (tt)
REVERT: B  317 CYS cc_start: 0.8214 (p) cc_final: 0.7878 (p)
REVERT: B  325 MET cc_start: 0.8319 (mmm) cc_final: 0.8096 (tpp)
REVERT: G   31 MET cc_start: 0.3409 (mtt) cc_final: 0.2526 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1906
  time to fit residues: 57.3026
Evaluate side-chains
  169 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0170
   chunk 7 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.4024

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS
A 213 HIS
B  91 HIS
B 230 ASN
** B 295 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.113235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.092761 restraints weight = 21559.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.095194 restraints weight = 13285.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096927 restraints weight = 9378.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.6269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7108  Z= 0.214
  Angle     :  0.728   8.970   9631  Z= 0.378
  Chirality :  0.047   0.294   1112
  Planarity :  0.006   0.066   1209
  Dihedral  :  5.481  77.821    955
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.44 (0.28), residues: 869
  helix:  0.91 (0.26), residues: 382
  sheet: -0.52 (0.38), residues: 173
  loop : -1.61 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B  82 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.021   0.002   PHE C 344 
 TYR   0.015   0.002   TYR B  85 
 ARG   0.014   0.001   ARG A 205 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  161 VAL cc_start: 0.8888 (t) cc_final: 0.8539 (p)
REVERT: C  234 LEU cc_start: 0.9055 (tt) cc_final: 0.8789 (mt)
REVERT: C  238 ILE cc_start: 0.7169 (tt) cc_final: 0.6837 (tt)
REVERT: C  250 MET cc_start: 0.8093 (ptm) cc_final: 0.7662 (ptm)
REVERT: C  346 PHE cc_start: 0.8627 (t80) cc_final: 0.8334 (t80)
REVERT: C  357 LEU cc_start: 0.9354 (mt) cc_final: 0.9138 (mt)
REVERT: C  364 ILE cc_start: 0.8324 (tt) cc_final: 0.8046 (tp)
REVERT: A   21 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8196 (ttm170)
REVERT: A   22 ASN cc_start: 0.8946 (m110) cc_final: 0.8532 (m110)
REVERT: A  209 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7966 (ttpp)
REVERT: B   45 MET cc_start: 0.7932 (mmp) cc_final: 0.7300 (mmm)
REVERT: B  123 ILE cc_start: 0.9100 (mm) cc_final: 0.8566 (pt)
REVERT: B  190 LEU cc_start: 0.9128 (tt) cc_final: 0.8755 (tt)
REVERT: B  289 TYR cc_start: 0.7790 (m-80) cc_final: 0.7562 (m-80)
REVERT: G   31 MET cc_start: 0.3466 (mtt) cc_final: 0.3189 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1929
  time to fit residues: 55.1264
Evaluate side-chains
  163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    0.0270
   chunk 67 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.9242

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS
B  91 HIS
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.113489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.093018 restraints weight = 21164.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.095475 restraints weight = 12911.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.097121 restraints weight = 9122.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.6402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7108  Z= 0.196
  Angle     :  0.718   9.087   9631  Z= 0.370
  Chirality :  0.045   0.169   1112
  Planarity :  0.005   0.063   1209
  Dihedral  :  5.400  76.649    955
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.44 (0.29), residues: 869
  helix:  0.91 (0.26), residues: 384
  sheet: -0.59 (0.39), residues: 175
  loop : -1.57 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP C 339 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.019   0.002   PHE C 344 
 TYR   0.016   0.002   TYR B 145 
 ARG   0.014   0.001   ARG A 208 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2505.78 seconds
wall clock time: 45 minutes 42.66 seconds (2742.66 seconds total)