Starting phenix.real_space_refine
on Sun May  3 00:45:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nzs_49958/05_2026/9nzs_49958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzs_49958/05_2026/9nzs_49958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzs_49958/05_2026/9nzs_49958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzs_49958/05_2026/9nzs_49958.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nzs_49958/05_2026/9nzs_49958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzs_49958/05_2026/9nzs_49958.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     170      5.49       5
     S      38      5.16       5
     C    5316      2.51       5
     N    1711      2.21       5
     O    2210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9446
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3295
          Classifications: {'peptide': 412}
          Link IDs: {'PTRANS': 10, 'TRANS': 401}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2548
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 9, 'TRANS': 306}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 533
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "D"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 163
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 2830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 2830
          Classifications: {'RNA': 132}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 64, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 19, 'rna3p': 112}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 76
          Classifications: {'DNA': 4}
          Link IDs: {'rna3p': 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2922  SG  CYS A 377      16.177  83.344  73.727  1.00 53.21           S
  ATOM   2945  SG  CYS A 380      13.708  85.149  72.047  1.00 54.55           S
  ATOM   3066  SG  CYS A 396      17.476  86.297  71.919  1.00 58.95           S
  ATOM   3088  SG  CYS A 399      15.577  86.910  75.066  1.00 51.27           S

  Time building chain proxies: 2.29, per 1000 atoms: 0.24
  Number of scatterers: 9446
  At special positions: 0
  Unit cell: (93.06, 112.8, 122.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      38     16.00
     P     170     15.00
     O    2210      8.00
     N    1711      7.00
     C    5316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 223.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 377 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 396 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 380 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 399 "
      Number of angles added : 6


  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      51.5% alpha, 9.9% beta
      52 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 62
      removed outlier: 3.709A  pdb=" N   ARG A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.748A  pdb=" N   GLU A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 3.863A  pdb=" N   HIS A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLY A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   GLN A  88 " --> pdb=" O   CYS A  84 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 3.585A  pdb=" N   LYS A 107 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 117
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 156 through 162
      removed outlier: 3.721A  pdb=" N   GLN A 162 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 188
      removed outlier: 4.281A  pdb=" N   PHE A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 271
      removed outlier: 3.564A  pdb=" N   LYS A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 4.272A  pdb=" N   GLY A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 319
      removed outlier: 4.135A  pdb=" N   ASP A 295 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   LYS A 296 " --> pdb=" O   GLN A 292 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A 297 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ALA A 298 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 361
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.612A  pdb=" N   ARG A 388 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 3.678A  pdb=" N   ILE A 415 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 427
      removed outlier: 3.929A  pdb=" N   ILE A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 54
      removed outlier: 4.500A  pdb=" N   GLU B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 87
      removed outlier: 4.446A  pdb=" N   GLY B  87 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 111
    Processing helix  chain 'B' and resid 111 through 117
    Processing helix  chain 'B' and resid 156 through 162
      removed outlier: 3.705A  pdb=" N   GLN B 162 " --> pdb=" O   PHE B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 188
    Processing helix  chain 'B' and resid 251 through 266
    Processing helix  chain 'B' and resid 294 through 319
    Processing helix  chain 'B' and resid 347 through 361
    Processing helix  chain 'B' and resid 407 through 415
      removed outlier: 4.163A  pdb=" N   ILE B 415 " --> pdb=" O   GLN B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 427
      removed outlier: 4.303A  pdb=" N   ASP B 419 " --> pdb=" O   ILE B 415 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 420 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA B 423 " --> pdb=" O   ASP B 419 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 133
      removed outlier: 3.678A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 198 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.856A  pdb=" N   ILE A 148 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 230
      removed outlier: 3.559A  pdb=" N   ASP A 228 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA A 234 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327
      removed outlier: 6.405A  pdb=" N   ILE A 324 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   ILE A 368 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   MET A 326 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 16
      removed outlier: 3.941A  pdb=" N   PHE B 205 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR B 199 " --> pdb=" O   PHE B 205 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU B 131 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 140
      removed outlier: 4.071A  pdb=" N   PHE B 169 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 247
      removed outlier: 3.977A  pdb=" N   VAL B 227 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   GLU B 327 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ILE B 324 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   ILE B 368 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   MET B 326 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)

    284 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      135 hydrogen bonds
      262 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.22 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: 1645
        1.33 -     1.45: 3393
        1.45 -     1.57: 4553
        1.57 -     1.69: 337
        1.69 -     1.82: 58
  Bond restraints: 9986
  Sorted by residual:
  bond pdb=" CA  THR A 189 "
       pdb=" CB  THR A 189 "
    ideal  model  delta    sigma   weight residual
    1.530  1.566 -0.036 1.54e-02 4.22e+03 5.43e+00
  bond pdb=" C3'  DA C  18 "
       pdb=" O3'  DA C  18 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.18e+00
  bond pdb=" CB  PHE B 300 "
       pdb=" CG  PHE B 300 "
    ideal  model  delta    sigma   weight residual
    1.502  1.554 -0.052 2.30e-02 1.89e+03 5.08e+00
  bond pdb=" CB  LYS A  11 "
       pdb=" CG  LYS A  11 "
    ideal  model  delta    sigma   weight residual
    1.520  1.461  0.059 3.00e-02 1.11e+03 3.88e+00
  bond pdb=" C   PRO B 213 "
       pdb=" N   PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.81e+00
  ... (remaining 9981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.79: 14179
        5.79 -    11.59: 73
       11.59 -    17.38: 5
       17.38 -    23.17: 2
       23.17 -    28.96: 1
  Bond angle restraints: 14260
  Sorted by residual:
  angle pdb=" O3'   A E  20 "
        pdb=" P     A E  21 "
        pdb=" OP1   A E  21 "
      ideal   model   delta    sigma   weight residual
     108.00   79.04   28.96 3.00e+00 1.11e-01 9.32e+01
  angle pdb=" CA  PRO B 214 "
        pdb=" N   PRO B 214 "
        pdb=" CD  PRO B 214 "
      ideal   model   delta    sigma   weight residual
     112.00  101.82   10.18 1.40e+00 5.10e-01 5.29e+01
  angle pdb=" CB  MET B 120 "
        pdb=" CG  MET B 120 "
        pdb=" SD  MET B 120 "
      ideal   model   delta    sigma   weight residual
     112.70  131.87  -19.17 3.00e+00 1.11e-01 4.08e+01
  angle pdb=" CA  MET B 120 "
        pdb=" CB  MET B 120 "
        pdb=" CG  MET B 120 "
      ideal   model   delta    sigma   weight residual
     114.10  126.84  -12.74 2.00e+00 2.50e-01 4.06e+01
  angle pdb=" O3'   A E  20 "
        pdb=" P     A E  21 "
        pdb=" OP2   A E  21 "
      ideal   model   delta    sigma   weight residual
     108.00   89.27   18.73 3.00e+00 1.11e-01 3.90e+01
  ... (remaining 14255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.71: 5349
       33.71 -    67.43: 657
       67.43 -   101.14: 68
      101.14 -   134.86: 4
      134.86 -   168.57: 5
  Dihedral angle restraints: 6083
    sinusoidal: 3965
      harmonic: 2118
  Sorted by residual:
  dihedral pdb=" O4'   C E  19 "
           pdb=" C1'   C E  19 "
           pdb=" N1    C E  19 "
           pdb=" C2    C E  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   52.44  147.56     1      1.50e+01 4.44e-03 7.87e+01
  dihedral pdb=" O4'   U E  86 "
           pdb=" C1'   U E  86 "
           pdb=" N1    U E  86 "
           pdb=" C2    U E  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   40.57 -168.57     1      1.70e+01 3.46e-03 6.58e+01
  dihedral pdb=" CA  GLY B 118 "
           pdb=" C   GLY B 118 "
           pdb=" N   SER B 119 "
           pdb=" CA  SER B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.39  -29.61     0      5.00e+00 4.00e-02 3.51e+01
  ... (remaining 6080 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.429: 1666
       0.429 -    0.858: 2
       0.858 -    1.287: 0
       1.287 -    1.716: 0
       1.716 -    2.145: 1
  Chirality restraints: 1669
  Sorted by residual:
  chirality pdb=" P     A E  21 "
            pdb=" OP1   A E  21 "
            pdb=" OP2   A E  21 "
            pdb=" O5'   A E  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.27    2.14 2.00e-01 2.50e+01 1.15e+02
  chirality pdb=" CG  LEU B 246 "
            pdb=" CB  LEU B 246 "
            pdb=" CD1 LEU B 246 "
            pdb=" CD2 LEU B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.05   -0.54 2.00e-01 2.50e+01 7.26e+00
  chirality pdb=" CG  LEU A 185 "
            pdb=" CB  LEU A 185 "
            pdb=" CD1 LEU A 185 "
            pdb=" CD2 LEU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.15   -0.44 2.00e-01 2.50e+01 4.86e+00
  ... (remaining 1666 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 212 "   -0.091 5.00e-02 4.00e+02   1.33e-01 2.83e+01
        pdb=" N   PRO A 213 "    0.230 5.00e-02 4.00e+02
        pdb=" CA  PRO A 213 "   -0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO A 213 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 213 "    0.078 5.00e-02 4.00e+02   1.17e-01 2.21e+01
        pdb=" N   PRO A 214 "   -0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO A 214 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A 214 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E 127 "    0.026 2.00e-02 2.50e+03   2.64e-02 2.09e+01
        pdb=" N9    G E 127 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    G E 127 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G E 127 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    G E 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G E 127 "   -0.014 2.00e-02 2.50e+03
        pdb=" O6    G E 127 "    0.021 2.00e-02 2.50e+03
        pdb=" N1    G E 127 "    0.012 2.00e-02 2.50e+03
        pdb=" C2    G E 127 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2    G E 127 "    0.039 2.00e-02 2.50e+03
        pdb=" N3    G E 127 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G E 127 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 3488
        2.92 -     3.41: 9291
        3.41 -     3.91: 17680
        3.91 -     4.40: 18773
        4.40 -     4.90: 27800
  Nonbonded interactions: 77032
  Sorted by model distance:
  nonbonded pdb=" N   ARG A 201 "
            pdb=" O   ARG A 201 "
     model   vdw
     2.420 2.496
  nonbonded pdb=" C3'   A E  20 "
            pdb=" OP2   A E  21 "
     model   vdw
     2.424 2.776
  nonbonded pdb=" N1    A E  34 "
            pdb=" O6    G E  64 "
     model   vdw
     2.446 2.496
  nonbonded pdb=" O5'   G E  28 "
            pdb=" O4'   G E  28 "
     model   vdw
     2.470 2.432
  nonbonded pdb=" O5'  DT C  19 "
            pdb=" O4'  DT C  19 "
     model   vdw
     2.490 2.432
  ... (remaining 77027 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:             2.990
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.930
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
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   9990  Z= 0.299
  Angle     :  1.257  28.965  14266  Z= 0.647
  Chirality :  0.079   2.145   1669
  Planarity :  0.011   0.133   1194
  Dihedral  : 24.387 168.571   4719
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 27.59 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.29), residues: 712
  helix:  0.95 (0.26), residues: 326
  sheet: -2.24 (0.49), residues: 98
  loop : -1.99 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.004   ARG A  38 
 TYR   0.034   0.003   TYR A  16 
 PHE   0.032   0.005   PHE B  23 
 TRP   0.049   0.004   TRP A  31 
 HIS   0.012   0.002   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 ( 9986)
  covalent geometry    : angle       1.24991 (14260)
  hydrogen bonds       : bond        0.14127 (  419)
  hydrogen bonds       : angle       5.53317 ( 1096)
  metal coordination   : bond        0.01162 (    4)
  metal coordination   : angle       6.71199 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 CYS cc_start: 0.6738 (m) cc_final: 0.6275 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1236
  time to fit residues: 16.0651
Evaluate side-chains
  68 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 166 ASN
A 273 HIS
A 281 HIS
A 404 ASN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 GLN
B 128 ASN
B 129 GLN
B 305 ASN
B 372 HIS
B 412 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.077958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.061442 restraints weight = 49989.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.063035 restraints weight = 24204.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.063977 restraints weight = 15878.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.064560 restraints weight = 12615.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.064840 restraints weight = 11089.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.122   9990  Z= 0.341
  Angle     :  0.879  27.611  14266  Z= 0.438
  Chirality :  0.065   1.996   1669
  Planarity :  0.007   0.080   1194
  Dihedral  : 25.168 156.445   3267
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 20.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 23.92 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.31), residues: 712
  helix:  1.43 (0.27), residues: 330
  sheet: -1.77 (0.50), residues: 113
  loop : -1.72 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 160 
 TYR   0.031   0.002   TYR A  16 
 PHE   0.017   0.003   PHE B 300 
 TRP   0.019   0.003   TRP A  31 
 HIS   0.004   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00720 ( 9986)
  covalent geometry    : angle       0.87310 (14260)
  hydrogen bonds       : bond        0.06521 (  419)
  hydrogen bonds       : angle       4.78224 ( 1096)
  metal coordination   : bond        0.01710 (    4)
  metal coordination   : angle       5.16128 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9038 (ptpt)
REVERT: A  217 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7279 (t-90)
REVERT: A  321 CYS cc_start: 0.7063 (m) cc_final: 0.6661 (m)
REVERT: B  116 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8516 (tt)
REVERT: B  249 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7086 (m-30)
  outliers start: 27
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0824
  time to fit residues: 10.7039
Evaluate side-chains
  73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 71 optimal weight:   30.0000
   chunk 50 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.079744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.063306 restraints weight = 49131.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.064957 restraints weight = 23360.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.065980 restraints weight = 15151.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.066576 restraints weight = 11886.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.066850 restraints weight = 10424.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9990  Z= 0.165
  Angle     :  0.758  27.926  14266  Z= 0.371
  Chirality :  0.063   2.032   1669
  Planarity :  0.005   0.064   1194
  Dihedral  : 25.054 164.470   3267
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 24.56 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.31), residues: 712
  helix:  1.84 (0.27), residues: 329
  sheet: -1.42 (0.52), residues: 102
  loop : -1.88 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  38 
 TYR   0.017   0.001   TYR A  16 
 PHE   0.015   0.002   PHE B 212 
 TRP   0.017   0.002   TRP B 345 
 HIS   0.005   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9986)
  covalent geometry    : angle       0.75415 (14260)
  hydrogen bonds       : bond        0.05332 (  419)
  hydrogen bonds       : angle       4.30433 ( 1096)
  metal coordination   : bond        0.00813 (    4)
  metal coordination   : angle       3.79891 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  217 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7327 (m-70)
REVERT: A  321 CYS cc_start: 0.7169 (m) cc_final: 0.6785 (m)
REVERT: B  116 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8594 (tt)
REVERT: B  260 MET cc_start: 0.8168 (mmm) cc_final: 0.7901 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0893
  time to fit residues: 9.9743
Evaluate side-chains
  72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 59 optimal weight:   30.0000
   chunk 56 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.075944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.058626 restraints weight = 52850.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.060215 restraints weight = 25624.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061153 restraints weight = 16904.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.061571 restraints weight = 13424.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.061947 restraints weight = 12087.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.124   9990  Z= 0.379
  Angle     :  0.905  27.661  14266  Z= 0.450
  Chirality :  0.067   2.044   1669
  Planarity :  0.007   0.094   1194
  Dihedral  : 25.136 158.086   3267
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 22.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 24.88 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.31), residues: 712
  helix:  1.35 (0.26), residues: 338
  sheet: -1.53 (0.50), residues: 108
  loop : -2.07 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 371 
 TYR   0.034   0.002   TYR A  16 
 PHE   0.023   0.003   PHE A  23 
 TRP   0.013   0.002   TRP B 105 
 HIS   0.031   0.002   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00802 ( 9986)
  covalent geometry    : angle       0.89766 (14260)
  hydrogen bonds       : bond        0.06907 (  419)
  hydrogen bonds       : angle       4.62744 ( 1096)
  metal coordination   : bond        0.02011 (    4)
  metal coordination   : angle       5.60126 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8779 (t0)
REVERT: A   26 MET cc_start: 0.8210 (tmm) cc_final: 0.7904 (tmm)
REVERT: A  135 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9160 (ptpt)
REVERT: A  217 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7244 (t-90)
REVERT: A  260 MET cc_start: 0.8633 (tpp) cc_final: 0.8430 (tpp)
REVERT: A  321 CYS cc_start: 0.7304 (m) cc_final: 0.6955 (m)
REVERT: B  116 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8672 (tt)
REVERT: B  260 MET cc_start: 0.8269 (mmm) cc_final: 0.8013 (mmm)
  outliers start: 24
  outliers final: 15
  residues processed: 82
  average time/residue: 0.0823
  time to fit residues: 10.0407
Evaluate side-chains
  76 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 67 optimal weight:   20.0000
   chunk 24 optimal weight:    0.3980
   chunk 0 optimal weight:    0.6980
   chunk 37 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.077084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.060470 restraints weight = 50880.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.062059 restraints weight = 24439.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.063041 restraints weight = 15974.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.063618 restraints weight = 12609.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.063804 restraints weight = 11121.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9990  Z= 0.192
  Angle     :  0.783  28.074  14266  Z= 0.382
  Chirality :  0.063   2.051   1669
  Planarity :  0.005   0.060   1194
  Dihedral  : 25.084 164.756   3267
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.16 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.31), residues: 712
  helix:  1.64 (0.26), residues: 338
  sheet: -1.41 (0.51), residues: 102
  loop : -2.06 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 301 
 TYR   0.017   0.002   TYR A  16 
 PHE   0.012   0.002   PHE B 212 
 TRP   0.014   0.002   TRP A  51 
 HIS   0.005   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9986)
  covalent geometry    : angle       0.77743 (14260)
  hydrogen bonds       : bond        0.05440 (  419)
  hydrogen bonds       : angle       4.15778 ( 1096)
  metal coordination   : bond        0.01028 (    4)
  metal coordination   : angle       4.48607 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9146 (ptpt)
REVERT: A  217 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7280 (m-70)
REVERT: A  321 CYS cc_start: 0.7070 (m) cc_final: 0.6686 (m)
REVERT: B  116 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8657 (tt)
REVERT: B  171 MET cc_start: 0.7027 (mmp) cc_final: 0.4947 (ttm)
REVERT: B  260 MET cc_start: 0.8252 (mmm) cc_final: 0.7999 (mmm)
  outliers start: 18
  outliers final: 13
  residues processed: 71
  average time/residue: 0.0831
  time to fit residues: 8.7153
Evaluate side-chains
  71 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0050
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.9800

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.080278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.063399 restraints weight = 55481.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.064993 restraints weight = 25907.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.065974 restraints weight = 16855.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.066497 restraints weight = 13385.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.066824 restraints weight = 11900.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9990  Z= 0.200
  Angle     :  0.763  28.097  14266  Z= 0.371
  Chirality :  0.063   2.058   1669
  Planarity :  0.005   0.058   1194
  Dihedral  : 24.970 165.823   3267
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 26.00 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.31), residues: 712
  helix:  1.75 (0.26), residues: 336
  sheet: -1.51 (0.49), residues: 108
  loop : -1.99 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 379 
 TYR   0.019   0.002   TYR A  16 
 PHE   0.013   0.002   PHE A 169 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.007   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9986)
  covalent geometry    : angle       0.75716 (14260)
  hydrogen bonds       : bond        0.05318 (  419)
  hydrogen bonds       : angle       4.05665 ( 1096)
  metal coordination   : bond        0.01037 (    4)
  metal coordination   : angle       4.60219 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9189 (ptpt)
REVERT: A  196 GLN cc_start: 0.8239 (mp10) cc_final: 0.7909 (mp10)
REVERT: A  217 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7350 (m-70)
REVERT: A  260 MET cc_start: 0.8554 (tpp) cc_final: 0.8293 (tpp)
REVERT: A  321 CYS cc_start: 0.6958 (m) cc_final: 0.6608 (m)
REVERT: B  116 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8687 (tt)
REVERT: B  171 MET cc_start: 0.7115 (mmp) cc_final: 0.5115 (ttm)
REVERT: B  196 GLN cc_start: 0.8083 (mt0) cc_final: 0.7696 (mm-40)
REVERT: B  249 ASP cc_start: 0.7837 (t0) cc_final: 0.7497 (m-30)
REVERT: B  260 MET cc_start: 0.8443 (mmm) cc_final: 0.8153 (mmm)
  outliers start: 24
  outliers final: 13
  residues processed: 79
  average time/residue: 0.0824
  time to fit residues: 9.6592
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.073377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.056132 restraints weight = 51311.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.057667 restraints weight = 24898.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.058600 restraints weight = 16445.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.059116 restraints weight = 13018.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.059378 restraints weight = 11512.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.106   9990  Z= 0.329
  Angle     :  0.870  28.131  14266  Z= 0.429
  Chirality :  0.066   2.067   1669
  Planarity :  0.005   0.060   1194
  Dihedral  : 25.035 162.429   3267
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 23.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.48 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.31), residues: 712
  helix:  1.16 (0.26), residues: 344
  sheet: -1.90 (0.46), residues: 112
  loop : -2.18 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 379 
 TYR   0.028   0.002   TYR A  16 
 PHE   0.017   0.002   PHE A 182 
 TRP   0.013   0.002   TRP B 105 
 HIS   0.006   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 ( 9986)
  covalent geometry    : angle       0.86148 (14260)
  hydrogen bonds       : bond        0.06747 (  419)
  hydrogen bonds       : angle       4.45810 ( 1096)
  metal coordination   : bond        0.01870 (    4)
  metal coordination   : angle       5.85393 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 57
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9176 (ptpt)
REVERT: A  217 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7155 (t-90)
REVERT: A  260 MET cc_start: 0.8602 (tpp) cc_final: 0.8198 (tpp)
REVERT: A  287 VAL cc_start: 0.9333 (m) cc_final: 0.8854 (p)
REVERT: A  296 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9028 (tttm)
REVERT: A  301 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.6718 (tpp-160)
REVERT: A  321 CYS cc_start: 0.7526 (m) cc_final: 0.7182 (m)
REVERT: B  189 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8698 (p)
REVERT: B  196 GLN cc_start: 0.8004 (mt0) cc_final: 0.7623 (mm-40)
REVERT: B  249 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7800 (m-30)
REVERT: B  260 MET cc_start: 0.8491 (mmm) cc_final: 0.8231 (mmm)
REVERT: B  370 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.8410 (Cg_exo)
  outliers start: 27
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0898
  time to fit residues: 10.3575
Evaluate side-chains
  79 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9980
   chunk 81 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.4144

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
B  29 GLN
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.075588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.058435 restraints weight = 49637.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.060077 restraints weight = 23328.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.061065 restraints weight = 15018.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.061638 restraints weight = 11741.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061902 restraints weight = 10269.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9990  Z= 0.167
  Angle     :  0.757  28.386  14266  Z= 0.368
  Chirality :  0.063   2.058   1669
  Planarity :  0.004   0.056   1194
  Dihedral  : 24.969 170.006   3267
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 27.43 %
    Favored  : 68.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.31), residues: 712
  helix:  1.62 (0.26), residues: 338
  sheet: -1.74 (0.47), residues: 112
  loop : -2.06 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 263 
 TYR   0.015   0.001   TYR A  16 
 PHE   0.033   0.002   PHE A  23 
 TRP   0.015   0.002   TRP A  51 
 HIS   0.003   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9986)
  covalent geometry    : angle       0.75136 (14260)
  hydrogen bonds       : bond        0.05213 (  419)
  hydrogen bonds       : angle       3.96295 ( 1096)
  metal coordination   : bond        0.00752 (    4)
  metal coordination   : angle       4.59797 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9220 (ptpt)
REVERT: A  196 GLN cc_start: 0.8280 (mp10) cc_final: 0.7932 (mp10)
REVERT: A  217 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7185 (t-90)
REVERT: A  260 MET cc_start: 0.8606 (tpp) cc_final: 0.8400 (tpp)
REVERT: A  296 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8910 (tttm)
REVERT: A  301 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.6654 (tpp-160)
REVERT: A  321 CYS cc_start: 0.7117 (m) cc_final: 0.6756 (m)
REVERT: B  171 MET cc_start: 0.7200 (mmp) cc_final: 0.5736 (mtt)
REVERT: B  189 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8526 (p)
REVERT: B  196 GLN cc_start: 0.8043 (mt0) cc_final: 0.7811 (mm-40)
REVERT: B  249 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (m-30)
REVERT: B  260 MET cc_start: 0.8499 (mmm) cc_final: 0.8223 (mmm)
REVERT: B  370 PRO cc_start: 0.8737 (Cg_exo) cc_final: 0.8449 (Cg_exo)
  outliers start: 24
  outliers final: 18
  residues processed: 82
  average time/residue: 0.0894
  time to fit residues: 10.6676
Evaluate side-chains
  84 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0270
   chunk 43 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0970
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   overall best weight:    2.0242

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.075214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.058075 restraints weight = 50134.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.059666 restraints weight = 24128.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.060590 restraints weight = 15797.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 65)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.061183 restraints weight = 12512.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.061443 restraints weight = 10992.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   9990  Z= 0.203
  Angle     :  0.764  28.304  14266  Z= 0.372
  Chirality :  0.063   2.059   1669
  Planarity :  0.005   0.058   1194
  Dihedral  : 24.881 168.664   3267
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 27.59 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.32), residues: 712
  helix:  1.75 (0.27), residues: 335
  sheet: -1.77 (0.46), residues: 112
  loop : -2.17 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 263 
 TYR   0.020   0.002   TYR A  16 
 PHE   0.027   0.002   PHE A  23 
 TRP   0.012   0.002   TRP A  51 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 9986)
  covalent geometry    : angle       0.75798 (14260)
  hydrogen bonds       : bond        0.05378 (  419)
  hydrogen bonds       : angle       3.97569 ( 1096)
  metal coordination   : bond        0.01029 (    4)
  metal coordination   : angle       4.79126 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9189 (ptpt)
REVERT: A  196 GLN cc_start: 0.8250 (mp10) cc_final: 0.7904 (mp10)
REVERT: A  217 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7084 (t-90)
REVERT: A  296 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8909 (tttm)
REVERT: A  301 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.6681 (tpp-160)
REVERT: A  321 CYS cc_start: 0.7281 (m) cc_final: 0.6930 (m)
REVERT: B  186 MET cc_start: 0.9017 (tpp) cc_final: 0.8811 (tpp)
REVERT: B  189 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8669 (p)
REVERT: B  249 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7948 (m-30)
REVERT: B  260 MET cc_start: 0.8519 (mmm) cc_final: 0.8242 (mmm)
REVERT: B  370 PRO cc_start: 0.8732 (Cg_endo) cc_final: 0.8436 (Cg_exo)
  outliers start: 24
  outliers final: 16
  residues processed: 82
  average time/residue: 0.0897
  time to fit residues: 10.5916
Evaluate side-chains
  82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.075635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.058394 restraints weight = 49961.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.060031 restraints weight = 23454.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.061027 restraints weight = 15183.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.061563 restraints weight = 11906.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.061877 restraints weight = 10488.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9990  Z= 0.183
  Angle     :  0.754  28.332  14266  Z= 0.365
  Chirality :  0.063   2.057   1669
  Planarity :  0.005   0.056   1194
  Dihedral  : 24.861 170.693   3267
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 27.75 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.32), residues: 712
  helix:  1.74 (0.26), residues: 342
  sheet: -1.74 (0.47), residues: 112
  loop : -2.17 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 160 
 TYR   0.018   0.001   TYR A  16 
 PHE   0.028   0.002   PHE A  23 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.003   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 9986)
  covalent geometry    : angle       0.74874 (14260)
  hydrogen bonds       : bond        0.05110 (  419)
  hydrogen bonds       : angle       3.88251 ( 1096)
  metal coordination   : bond        0.00858 (    4)
  metal coordination   : angle       4.59772 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9186 (ptpt)
REVERT: A  196 GLN cc_start: 0.8254 (mp10) cc_final: 0.7909 (mp10)
REVERT: A  217 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7132 (t-90)
REVERT: A  258 LYS cc_start: 0.9285 (tmmt) cc_final: 0.8959 (tmmt)
REVERT: A  296 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8937 (tttm)
REVERT: A  301 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.6667 (tpp-160)
REVERT: A  321 CYS cc_start: 0.7274 (m) cc_final: 0.6905 (m)
REVERT: B  171 MET cc_start: 0.7294 (mmp) cc_final: 0.5761 (mtt)
REVERT: B  186 MET cc_start: 0.9042 (tpp) cc_final: 0.8827 (tpp)
REVERT: B  189 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8677 (p)
REVERT: B  196 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7555 (mt0)
REVERT: B  249 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7914 (m-30)
REVERT: B  260 MET cc_start: 0.8531 (mmm) cc_final: 0.8248 (mmm)
REVERT: B  370 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8449 (Cg_exo)
  outliers start: 23
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0863
  time to fit residues: 10.0754
Evaluate side-chains
  82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 CYS
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.074900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.057687 restraints weight = 50222.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.059300 restraints weight = 23744.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.060275 restraints weight = 15464.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.060883 restraints weight = 12095.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.061158 restraints weight = 10562.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   9990  Z= 0.220
  Angle     :  0.781  28.371  14266  Z= 0.380
  Chirality :  0.063   2.052   1669
  Planarity :  0.005   0.057   1194
  Dihedral  : 24.855 168.871   3267
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 27.59 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.32), residues: 712
  helix:  1.67 (0.27), residues: 342
  sheet: -1.82 (0.46), residues: 112
  loop : -2.26 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 263 
 TYR   0.021   0.002   TYR A  16 
 PHE   0.029   0.002   PHE A  23 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.004   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9986)
  covalent geometry    : angle       0.77446 (14260)
  hydrogen bonds       : bond        0.05380 (  419)
  hydrogen bonds       : angle       3.98557 ( 1096)
  metal coordination   : bond        0.01080 (    4)
  metal coordination   : angle       4.86082 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1717.36 seconds
wall clock time: 30 minutes 31.64 seconds (1831.64 seconds total)