Starting phenix.real_space_refine
on Thu Jun  5 23:39:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0r_23101/06_2025/7l0r_23101.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0r_23101/06_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_23101/06_2025/7l0r_23101.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0r_23101/06_2025/7l0r_23101.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0r_23101/06_2025/7l0r_23101.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0r_23101/06_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-5710/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: 4.40, per 1000 atoms: 0.63
  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: 1.72
  Conformation dependent library (CDL) restraints added in 919.0 milliseconds
  

  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: 0.67
  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: 1.93

  Time building geometry restraints manager: 2.05 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:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.230
  Find NCS groups from input model:        0.080
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.700
-------------------------------------------------------------------------------
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   7109  Z= 0.376
  Angle     :  1.372  10.325   9633  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12914 (  364)
  hydrogen bonds       : angle       7.58938 ( 1062)
  SS BOND              : bond        0.00362 (    1)
  SS BOND              : angle       1.86174 (    2)
  covalent geometry    : bond        0.00745 ( 7108)
  covalent geometry    : angle       1.37215 ( 9631)

*********************** 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  : 0.730 
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: 0.2468
  time to fit residues: 94.0236
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  : 0.764 
-------------------------------------------------------------------------------
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 = 0.091626 restraints weight = 21102.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.094157 restraints weight = 13057.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.095946 restraints weight = 9258.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
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   7109  Z= 0.146
  Angle     :  0.708   8.937   9633  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05145 (  364)
  hydrogen bonds       : angle       5.86851 ( 1062)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       1.06807 (    2)
  covalent geometry    : bond        0.00296 ( 7108)
  covalent geometry    : angle       0.70743 ( 9631)

*********************** 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  : 0.874 
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: 0.8401 (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: 0.9203 (tt) cc_final: 0.8852 (mt)
REVERT: C  345 ASP cc_start: 0.8385 (m-30) cc_final: 0.7814 (m-30)
REVERT: C  346 PHE cc_start: 0.8799 (t80) cc_final: 0.8452 (t80)
REVERT: C  357 LEU cc_start: 0.9367 (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: 0.7788 (pp30) cc_final: 0.7430 (pp30)
REVERT: A  243 MET cc_start: 0.8336 (tpp) cc_final: 0.7868 (tpp)
REVERT: A  343 ILE cc_start: 0.9251 (tp) cc_final: 0.9022 (tp)
REVERT: B   59 TYR cc_start: 0.8393 (m-80) cc_final: 0.7920 (m-80)
REVERT: B   61 MET cc_start: 0.7834 (ppp) cc_final: 0.7552 (ppp)
REVERT: B  149 CYS cc_start: 0.8086 (p) cc_final: 0.7725 (m)
REVERT: B  212 ASP cc_start: 0.5669 (t0) cc_final: 0.4701 (t0)
REVERT: B  261 LEU cc_start: 0.8818 (tt) cc_final: 0.8524 (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: 0.2028
  time to fit residues: 71.9022
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  : 0.812 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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 269 ASN
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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.108689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.088095 restraints weight = 22031.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.090587 restraints weight = 13477.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.092189 restraints weight = 9562.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7109  Z= 0.191
  Angle     :  0.703   7.522   9633  Z= 0.375
  Chirality :  0.046   0.189   1112
  Planarity :  0.005   0.051   1209
  Dihedral  :  5.512  62.124    955
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.63 %
    Favored  : 94.11 %
  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: 376
  sheet: -1.42 (0.35), residues: 181
  loop : -2.15 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  82 
 HIS   0.009   0.001   HIS B 311 
 PHE   0.022   0.002   PHE C 344 
 TYR   0.017   0.002   TYR C 349 
 ARG   0.004   0.001   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (  364)
  hydrogen bonds       : angle       5.68368 ( 1062)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       1.98138 (    2)
  covalent geometry    : bond        0.00400 ( 7108)
  covalent geometry    : angle       0.70256 ( 9631)

*********************** 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
  246 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8317 (mtp85)
REVERT: C  234 LEU cc_start: 0.9219 (tt) cc_final: 0.8845 (mt)
REVERT: C  250 MET cc_start: 0.8044 (ptm) cc_final: 0.7834 (ptm)
REVERT: C  345 ASP cc_start: 0.8471 (m-30) cc_final: 0.7892 (m-30)
REVERT: C  346 PHE cc_start: 0.8811 (t80) cc_final: 0.8539 (t80)
REVERT: A   18 MET cc_start: 0.8592 (tpp) cc_final: 0.8038 (tpp)
REVERT: A   21 ARG cc_start: 0.8668 (ttm170) cc_final: 0.8239 (ttm170)
REVERT: A   28 GLU cc_start: 0.8062 (tt0) cc_final: 0.7778 (tm-30)
REVERT: A  333 GLN cc_start: 0.8105 (pm20) cc_final: 0.7720 (pm20)
REVERT: B   61 MET cc_start: 0.7830 (ppp) cc_final: 0.7615 (ppp)
REVERT: B   82 TRP cc_start: 0.7908 (m-10) cc_final: 0.7465 (m-10)
REVERT: B  118 ASP cc_start: 0.8274 (p0) cc_final: 0.7934 (p0)
REVERT: G   41 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7898 (ttp80)
REVERT: G   42 ASP cc_start: 0.8716 (p0) cc_final: 0.7854 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 244
  average time/residue: 0.2257
  time to fit residues: 71.5267
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  : 0.837 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 51 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7362

-------------------------------------------------------------------------------
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
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3877 r_free = 0.3877 target = 0.112181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.091509 restraints weight = 21250.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.094313 restraints weight = 12368.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.096204 restraints weight = 8416.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.4780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7109  Z= 0.137
  Angle     :  0.658   8.110   9633  Z= 0.347
  Chirality :  0.045   0.276   1112
  Planarity :  0.004   0.052   1209
  Dihedral  :  5.331  59.549    955
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.93 %
    Favored  : 95.94 %
  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 (0.28), residues: 869
  helix:  0.74 (0.26), residues: 376
  sheet: -0.91 (0.36), residues: 179
  loop : -2.06 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.022   0.002   PHE A 307 
 TYR   0.020   0.001   TYR B 145 
 ARG   0.008   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04533 (  364)
  hydrogen bonds       : angle       5.45440 ( 1062)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       1.15345 (    2)
  covalent geometry    : bond        0.00281 ( 7108)
  covalent geometry    : angle       0.65780 ( 9631)

*********************** 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
  262 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  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: symmetry clash
   revert: symmetry clash
REVERT: C  167 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8245 (mtp85)
REVERT: C  234 LEU cc_start: 0.9198 (tt) cc_final: 0.8825 (mt)
REVERT: C  250 MET cc_start: 0.8034 (ptm) cc_final: 0.7674 (ptm)
REVERT: C  305 ARG cc_start: 0.8827 (mtt90) cc_final: 0.8364 (mtt-85)
REVERT: C  327 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8000 (ttp80)
REVERT: C  345 ASP cc_start: 0.8469 (m-30) cc_final: 0.7822 (m-30)
REVERT: C  346 PHE cc_start: 0.8805 (t80) cc_final: 0.8555 (t80)
REVERT: C  357 LEU cc_start: 0.9366 (mt) cc_final: 0.9145 (mt)
REVERT: A   22 ASN cc_start: 0.9041 (m110) cc_final: 0.8526 (m110)
REVERT: A   28 GLU cc_start: 0.8077 (tt0) cc_final: 0.7771 (tm-30)
REVERT: A  204 GLN cc_start: 0.7871 (pp30) cc_final: 0.7493 (pp30)
REVERT: A  209 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8207 (ttpp)
REVERT: A  333 GLN cc_start: 0.8018 (pm20) cc_final: 0.7799 (pm20)
REVERT: B   45 MET cc_start: 0.7844 (mmp) cc_final: 0.7000 (tpp)
REVERT: B   61 MET cc_start: 0.7867 (ppp) cc_final: 0.7510 (ppp)
REVERT: B  118 ASP cc_start: 0.8246 (p0) cc_final: 0.7955 (p0)
REVERT: B  217 MET cc_start: 0.7865 (ttm) cc_final: 0.7650 (ppp)
REVERT: B  289 TYR cc_start: 0.7889 (m-80) cc_final: 0.7595 (m-80)
REVERT: G   38 GLU cc_start: 0.8388 (tp30) cc_final: 0.6840 (tp30)
REVERT: G   41 ARG cc_start: 0.8376 (tmm160) cc_final: 0.7999 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 261
  average time/residue: 0.2409
  time to fit residues: 81.2923
Evaluate side-chains
  194 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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  52 GLN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.111708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.091143 restraints weight = 21533.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.093774 restraints weight = 13209.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.095566 restraints weight = 9288.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7109  Z= 0.142
  Angle     :  0.661   7.225   9633  Z= 0.345
  Chirality :  0.045   0.284   1112
  Planarity :  0.004   0.053   1209
  Dihedral  :  5.209  56.901    955
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.88 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.65 (0.28), residues: 869
  helix:  0.96 (0.27), residues: 372
  sheet: -0.82 (0.37), residues: 175
  loop : -1.83 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 297 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.020   0.002   PHE C 344 
 TYR   0.018   0.002   TYR C 349 
 ARG   0.010   0.001   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  364)
  hydrogen bonds       : angle       5.36163 ( 1062)
  SS BOND              : bond        0.00265 (    1)
  SS BOND              : angle       2.81588 (    2)
  covalent geometry    : bond        0.00298 ( 7108)
  covalent geometry    : angle       0.65938 ( 9631)

*********************** 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
  232 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 0.882 
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  234 LEU cc_start: 0.9187 (tt) cc_final: 0.8823 (mt)
REVERT: C  250 MET cc_start: 0.7984 (ptm) cc_final: 0.7542 (ptm)
REVERT: C  345 ASP cc_start: 0.8460 (m-30) cc_final: 0.7663 (m-30)
REVERT: C  346 PHE cc_start: 0.8736 (t80) cc_final: 0.8400 (t80)
REVERT: C  357 LEU cc_start: 0.9320 (mt) cc_final: 0.9077 (mt)
REVERT: A   28 GLU cc_start: 0.8005 (tt0) cc_final: 0.7772 (tm-30)
REVERT: A  209 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8122 (ttpp)
REVERT: A  343 ILE cc_start: 0.9261 (tp) cc_final: 0.8849 (tp)
REVERT: A  347 ASN cc_start: 0.8417 (m110) cc_final: 0.8022 (m110)
REVERT: B   45 MET cc_start: 0.7807 (mmp) cc_final: 0.6971 (mmt)
REVERT: B   61 MET cc_start: 0.7887 (ppp) cc_final: 0.7588 (ppp)
REVERT: B  118 ASP cc_start: 0.8254 (p0) cc_final: 0.7989 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2686
  time to fit residues: 82.0626
Evaluate side-chains
  175 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 127 ASN
C 257 ASN
C 325 HIS
** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  52 GLN
A 213 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 266 HIS
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.107016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.086191 restraints weight = 22122.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.088799 restraints weight = 12981.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.090553 restraints weight = 8970.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.5438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7109  Z= 0.188
  Angle     :  0.694   7.873   9633  Z= 0.364
  Chirality :  0.046   0.292   1112
  Planarity :  0.005   0.052   1209
  Dihedral  :  5.287  55.754    955
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  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: -0.50 (0.29), residues: 869
  helix:  1.05 (0.27), residues: 376
  sheet: -0.84 (0.38), residues: 184
  loop : -1.68 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 297 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.044   0.002   PHE C 344 
 TYR   0.020   0.002   TYR C 333 
 ARG   0.011   0.001   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04516 (  364)
  hydrogen bonds       : angle       5.27235 ( 1062)
  SS BOND              : bond        0.00199 (    1)
  SS BOND              : angle       0.98427 (    2)
  covalent geometry    : bond        0.00401 ( 7108)
  covalent geometry    : angle       0.69375 ( 9631)

*********************** 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
  226 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 224
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.6847 (m-40) cc_final: 0.6555 (m-40)
REVERT: C  149 ARG cc_start: 0.7074 (tmm160) cc_final: 0.6822 (tpt90)
REVERT: C  166 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: C  234 LEU cc_start: 0.9195 (tt) cc_final: 0.8843 (mt)
REVERT: C  250 MET cc_start: 0.7982 (ptm) cc_final: 0.7567 (ptm)
REVERT: C  305 ARG cc_start: 0.8823 (mtt90) cc_final: 0.8371 (mtt-85)
REVERT: C  327 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8120 (ttp80)
REVERT: C  345 ASP cc_start: 0.8444 (m-30) cc_final: 0.7985 (p0)
REVERT: C  346 PHE cc_start: 0.8780 (t80) cc_final: 0.8392 (t80)
REVERT: C  357 LEU cc_start: 0.9384 (mt) cc_final: 0.9161 (mt)
REVERT: C  364 ILE cc_start: 0.8349 (tt) cc_final: 0.8122 (tp)
REVERT: A   22 ASN cc_start: 0.9015 (m110) cc_final: 0.8708 (m110)
REVERT: A  195 HIS cc_start: 0.7144 (p90) cc_final: 0.6917 (p-80)
REVERT: A  197 LYS cc_start: 0.7737 (mptt) cc_final: 0.7471 (mmtt)
REVERT: A  209 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8074 (ttpp)
REVERT: B   45 MET cc_start: 0.7882 (mmp) cc_final: 0.7389 (tpp)
REVERT: B   74 SER cc_start: 0.9149 (p) cc_final: 0.8757 (t)
REVERT: B  118 ASP cc_start: 0.8361 (p0) cc_final: 0.8132 (p0)
REVERT: B  129 ARG cc_start: 0.8615 (ppt170) cc_final: 0.8222 (ttp80)
  outliers start: 2
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2044
  time to fit residues: 60.3964
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  : 1.300 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0570
   chunk 54 optimal weight:    0.1980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.4504

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

Flipped N/Q/H residues before XYZ refinement:
C 257 ASN
C 325 HIS
B 142 HIS
B 175 GLN
B 230 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.108774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.088455 restraints weight = 21878.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090947 restraints weight = 13293.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.092668 restraints weight = 9299.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7109  Z= 0.151
  Angle     :  0.682   8.097   9633  Z= 0.356
  Chirality :  0.045   0.259   1112
  Planarity :  0.005   0.064   1209
  Dihedral  :  5.327  67.077    955
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.62 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.49 (0.29), residues: 869
  helix:  0.99 (0.26), residues: 380
  sheet: -0.80 (0.38), residues: 184
  loop : -1.65 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  82 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.021   0.002   PHE C 344 
 TYR   0.012   0.002   TYR B 145 
 ARG   0.012   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04401 (  364)
  hydrogen bonds       : angle       5.27500 ( 1062)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       1.45563 (    2)
  covalent geometry    : bond        0.00325 ( 7108)
  covalent geometry    : angle       0.68185 ( 9631)

*********************** 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
  232 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.6918 (m-40) cc_final: 0.6638 (m-40)
REVERT: C  234 LEU cc_start: 0.9158 (tt) cc_final: 0.8822 (mt)
REVERT: C  238 ILE cc_start: 0.7201 (tt) cc_final: 0.6891 (tt)
REVERT: C  250 MET cc_start: 0.8018 (ptm) cc_final: 0.7628 (ptm)
REVERT: C  345 ASP cc_start: 0.8416 (m-30) cc_final: 0.8039 (p0)
REVERT: C  346 PHE cc_start: 0.8701 (t80) cc_final: 0.8341 (t80)
REVERT: C  357 LEU cc_start: 0.9348 (mt) cc_final: 0.9122 (mt)
REVERT: C  364 ILE cc_start: 0.8248 (tt) cc_final: 0.7995 (tp)
REVERT: A   22 ASN cc_start: 0.8881 (m110) cc_final: 0.8616 (m110)
REVERT: A  197 LYS cc_start: 0.7783 (mptt) cc_final: 0.7477 (mmtt)
REVERT: A  209 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8031 (ttpp)
REVERT: A  247 MET cc_start: 0.7616 (mtm) cc_final: 0.7174 (mtm)
REVERT: A  316 THR cc_start: 0.8312 (p) cc_final: 0.8102 (p)
REVERT: B   45 MET cc_start: 0.7808 (mmp) cc_final: 0.7343 (tpp)
REVERT: B  230 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (m-40)
REVERT: B  246 ASP cc_start: 0.8707 (m-30) cc_final: 0.8345 (m-30)
REVERT: B  260 GLU cc_start: 0.7219 (tp30) cc_final: 0.6157 (mp0)
REVERT: G   35 LYS cc_start: 0.9096 (ptmt) cc_final: 0.8621 (pptt)
REVERT: G   37 CYS cc_start: 0.8645 (m) cc_final: 0.8141 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1927
  time to fit residues: 59.9704
Evaluate side-chains
  168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 58 optimal weight:    0.1980
   chunk 43 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    0.1980
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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
A  52 GLN
** A 322 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 = 0.3823 r_free = 0.3823 target = 0.108322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.087983 restraints weight = 22091.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.090503 restraints weight = 13269.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.092250 restraints weight = 9215.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.5812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7109  Z= 0.162
  Angle     :  0.702   8.351   9633  Z= 0.364
  Chirality :  0.046   0.263   1112
  Planarity :  0.005   0.057   1209
  Dihedral  :  5.333  61.728    955
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  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: -0.33 (0.29), residues: 869
  helix:  1.11 (0.26), residues: 373
  sheet: -0.56 (0.39), residues: 183
  loop : -1.59 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 297 
 HIS   0.008   0.001   HIS A 195 
 PHE   0.021   0.002   PHE C 344 
 TYR   0.019   0.002   TYR B  85 
 ARG   0.013   0.001   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04426 (  364)
  hydrogen bonds       : angle       5.24267 ( 1062)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       3.87799 (    2)
  covalent geometry    : bond        0.00349 ( 7108)
  covalent geometry    : angle       0.70001 ( 9631)

*********************** 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
  218 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.892 
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: 0.6855 (m-40) cc_final: 0.6598 (m-40)
REVERT: C  166 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7525 (tm-30)
REVERT: C  234 LEU cc_start: 0.9144 (tt) cc_final: 0.8813 (mt)
REVERT: C  238 ILE cc_start: 0.7176 (tt) cc_final: 0.6856 (tt)
REVERT: C  250 MET cc_start: 0.8007 (ptm) cc_final: 0.7609 (ptm)
REVERT: C  345 ASP cc_start: 0.8452 (m-30) cc_final: 0.7980 (p0)
REVERT: C  346 PHE cc_start: 0.8680 (t80) cc_final: 0.8292 (t80)
REVERT: C  357 LEU cc_start: 0.9351 (mt) cc_final: 0.9121 (mt)
REVERT: C  364 ILE cc_start: 0.8192 (tt) cc_final: 0.7916 (tp)
REVERT: A   22 ASN cc_start: 0.8924 (m110) cc_final: 0.8630 (m110)
REVERT: A  206 SER cc_start: 0.7545 (p) cc_final: 0.7297 (p)
REVERT: A  209 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8042 (ttpp)
REVERT: B   45 MET cc_start: 0.7824 (mmp) cc_final: 0.7361 (tpp)
REVERT: B  118 ASP cc_start: 0.8135 (p0) cc_final: 0.7854 (p0)
REVERT: B  123 ILE cc_start: 0.9118 (mm) cc_final: 0.8642 (pt)
REVERT: B  129 ARG cc_start: 0.8560 (ppt170) cc_final: 0.8190 (ttp80)
REVERT: B  190 LEU cc_start: 0.9141 (tt) cc_final: 0.8772 (tt)
REVERT: B  246 ASP cc_start: 0.8654 (m-30) cc_final: 0.8362 (m-30)
REVERT: B  260 GLU cc_start: 0.7295 (tp30) cc_final: 0.6316 (mp0)
REVERT: B  325 MET cc_start: 0.8335 (mmm) cc_final: 0.8133 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.1808
  time to fit residues: 53.4349
Evaluate side-chains
  164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    0.4980
   chunk 7 optimal weight:    5.9990
   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 325 HIS
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.110838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090921 restraints weight = 21782.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093470 restraints weight = 13132.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.095193 restraints weight = 9127.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.6022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7109  Z= 0.135
  Angle     :  0.682   8.577   9633  Z= 0.349
  Chirality :  0.045   0.234   1112
  Planarity :  0.005   0.058   1209
  Dihedral  :  5.158  59.101    955
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.39 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.29), residues: 869
  helix:  0.99 (0.26), residues: 383
  sheet: -0.25 (0.41), residues: 167
  loop : -1.53 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.008   0.001   HIS A 195 
 PHE   0.022   0.002   PHE B 253 
 TYR   0.016   0.002   TYR B  85 
 ARG   0.013   0.001   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  364)
  hydrogen bonds       : angle       5.16006 ( 1062)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       2.49701 (    2)
  covalent geometry    : bond        0.00288 ( 7108)
  covalent geometry    : angle       0.68154 ( 9631)

*********************** 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
  231 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.6815 (m-40) cc_final: 0.6597 (m-40)
REVERT: C  161 VAL cc_start: 0.8872 (t) cc_final: 0.8541 (p)
REVERT: C  166 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: C  234 LEU cc_start: 0.9093 (tt) cc_final: 0.8816 (mt)
REVERT: C  238 ILE cc_start: 0.7125 (tt) cc_final: 0.6787 (tt)
REVERT: C  250 MET cc_start: 0.7974 (ptm) cc_final: 0.7552 (ptm)
REVERT: C  345 ASP cc_start: 0.8395 (m-30) cc_final: 0.7943 (p0)
REVERT: C  346 PHE cc_start: 0.8652 (t80) cc_final: 0.8274 (t80)
REVERT: C  357 LEU cc_start: 0.9344 (mt) cc_final: 0.9117 (mt)
REVERT: C  364 ILE cc_start: 0.8067 (tt) cc_final: 0.7794 (tp)
REVERT: A   22 ASN cc_start: 0.8887 (m110) cc_final: 0.8548 (m110)
REVERT: A  209 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7967 (ttpp)
REVERT: B   45 MET cc_start: 0.7883 (mmp) cc_final: 0.7242 (mmm)
REVERT: B   61 MET cc_start: 0.7859 (ppp) cc_final: 0.7572 (ppp)
REVERT: B  118 ASP cc_start: 0.8134 (p0) cc_final: 0.7803 (p0)
REVERT: B  123 ILE cc_start: 0.9117 (mm) cc_final: 0.8665 (pt)
REVERT: B  129 ARG cc_start: 0.8566 (ppt170) cc_final: 0.8214 (ttp80)
REVERT: B  190 LEU cc_start: 0.9093 (tt) cc_final: 0.8735 (tt)
REVERT: B  289 TYR cc_start: 0.7871 (m-80) cc_final: 0.7382 (m-80)
REVERT: B  318 LEU cc_start: 0.8539 (pp) cc_final: 0.8338 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1723
  time to fit residues: 53.8740
Evaluate side-chains
  175 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0870
   chunk 50 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS
A 306 GLN
B 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.111250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.090874 restraints weight = 21962.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.093451 restraints weight = 13258.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.095203 restraints weight = 9239.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.6233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7109  Z= 0.132
  Angle     :  0.683   8.786   9633  Z= 0.346
  Chirality :  0.044   0.154   1112
  Planarity :  0.005   0.061   1209
  Dihedral  :  5.022  54.951    955
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.52 %
    Favored  : 99.35 %
  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 (0.29), residues: 869
  helix:  1.05 (0.26), residues: 385
  sheet: -0.27 (0.40), residues: 173
  loop : -1.44 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 339 
 HIS   0.008   0.001   HIS A 195 
 PHE   0.023   0.002   PHE A 250 
 TYR   0.017   0.001   TYR C 105 
 ARG   0.014   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  364)
  hydrogen bonds       : angle       5.09406 ( 1062)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       2.71998 (    2)
  covalent geometry    : bond        0.00279 ( 7108)
  covalent geometry    : angle       0.68235 ( 9631)

********************** 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
  222 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: C  234 LEU cc_start: 0.9071 (tt) cc_final: 0.8806 (mt)
REVERT: C  238 ILE cc_start: 0.7071 (tt) cc_final: 0.6734 (tt)
REVERT: C  250 MET cc_start: 0.7973 (ptm) cc_final: 0.7541 (ptm)
REVERT: C  345 ASP cc_start: 0.8398 (m-30) cc_final: 0.7931 (p0)
REVERT: C  346 PHE cc_start: 0.8646 (t80) cc_final: 0.8276 (t80)
REVERT: C  357 LEU cc_start: 0.9355 (mt) cc_final: 0.9137 (mt)
REVERT: C  364 ILE cc_start: 0.8053 (tt) cc_final: 0.7745 (tp)
REVERT: A   22 ASN cc_start: 0.8905 (m110) cc_final: 0.8470 (m110)
REVERT: A  209 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7974 (ttpp)
REVERT: B   45 MET cc_start: 0.7874 (mmp) cc_final: 0.7253 (mmm)
REVERT: B  118 ASP cc_start: 0.8198 (p0) cc_final: 0.7831 (p0)
REVERT: B  123 ILE cc_start: 0.9108 (mm) cc_final: 0.8620 (pt)
REVERT: B  129 ARG cc_start: 0.8538 (ppt170) cc_final: 0.8188 (ttp80)
REVERT: B  190 LEU cc_start: 0.9041 (tt) cc_final: 0.8706 (tt)
REVERT: B  260 GLU cc_start: 0.7019 (tp30) cc_final: 0.6113 (mp0)
REVERT: B  289 TYR cc_start: 0.7862 (m-80) cc_final: 0.7267 (m-80)
REVERT: G   37 CYS cc_start: 0.8486 (m) cc_final: 0.7968 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1818
  time to fit residues: 54.3638
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  : 0.863 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
C 325 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.109883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.090341 restraints weight = 21983.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.092754 restraints weight = 13486.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.094416 restraints weight = 9480.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.6342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7109  Z= 0.159
  Angle     :  0.714   8.786   9633  Z= 0.365
  Chirality :  0.046   0.256   1112
  Planarity :  0.005   0.066   1209
  Dihedral  :  5.145  52.708    955
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.29), residues: 869
  helix:  1.10 (0.26), residues: 379
  sheet: -0.43 (0.39), residues: 180
  loop : -1.29 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 297 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.020   0.002   PHE B 234 
 TYR   0.015   0.002   TYR C 105 
 ARG   0.013   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 (  364)
  hydrogen bonds       : angle       5.14799 ( 1062)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       2.37625 (    2)
  covalent geometry    : bond        0.00350 ( 7108)
  covalent geometry    : angle       0.71303 ( 9631)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2835.37 seconds
wall clock time: 51 minutes 4.35 seconds (3064.35 seconds total)