Starting phenix.real_space_refine
on Fri Sep 11 00:27:50 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9l_27265/09_2026/8d9l_27265.map"
  }
  resolution = 4.04
  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=   0.003 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     S      23      5.16       5
     C    3418      2.51       5
     N    1000      2.21       5
     O    1251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5757
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2557
          Classifications: {'peptide': 332}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1783
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 204}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 1390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1390
          Classifications: {'RNAv2': 65}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 28, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 10, 'rna3p': 54}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Residues with excluded nonbonded symmetry interactions: 40
    residue:
      pdb=" N   GLN B  12 " occ=0.85
      ... (7 atoms not shown)
      pdb=" NE2 GLN B  12 " occ=0.85
    residue:
      pdb=" N   ARG B  21 " occ=0.88
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  21 " occ=0.88
    residue:
      pdb=" N   CYS B  40 " occ=0.68
      ... (4 atoms not shown)
      pdb=" SG  CYS B  40 " occ=0.68
    residue:
      pdb=" N   SER B  61 " occ=0.82
      ... (4 atoms not shown)
      pdb=" OG  SER B  61 " occ=0.82
    residue:
      pdb=" N   ASP B  80 " occ=0.85
      ... (6 atoms not shown)
      pdb=" OD2 ASP B  80 " occ=0.85
    residue:
      pdb=" N   ASP B  81 " occ=0.80
      ... (6 atoms not shown)
      pdb=" OD2 ASP B  81 " occ=0.80
    residue:
      pdb=" N   ARG B  84 " occ=0.91
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  84 " occ=0.91
    residue:
      pdb=" N   ARG B  89 " occ=0.99
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  89 " occ=0.99
    residue:
      pdb=" N   CYS B 105 " occ=0.82
      ... (4 atoms not shown)
      pdb=" SG  CYS B 105 " occ=0.82
    residue:
      pdb=" N   LYS B 122 " occ=0.88
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 122 " occ=0.88
    residue:
      pdb=" N   GLU B 133 " occ=0.89
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 133 " occ=0.89
    residue:
      pdb=" N   CYS B 137 " occ=0.86
      ... (4 atoms not shown)
      pdb=" SG  CYS B 137 " occ=0.86
    ... (remaining 28 not shown)
  Time building chain proxies: 1.52, per 1000 atoms: 0.26
  Number of scatterers: 5757
  At special positions: 0
  Unit cell: (65.52, 98.28, 112.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P      65     15.00
     O    1251      8.00
     N    1000      7.00
     C    3418      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: 0.54
  Conformation dependent library (CDL) restraints added in 385.1 milliseconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1032

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 8 sheets defined
      19.0% alpha, 32.2% beta
      27 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.516A  pdb=" N   GLN B 233 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 233'
    Processing helix  chain 'B' and resid 330 through 343
    Processing helix  chain 'B' and resid 353 through 359
      removed outlier: 3.817A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 109 through 126
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.830A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
      removed outlier: 3.513A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.907A  pdb=" N   SER A 226 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 235
      removed outlier: 4.256A  pdb=" N   GLY A 232 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLY A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 69
      removed outlier: 7.107A  pdb=" N   THR B  79 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA B  77 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   PHE B  69 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   TYR B  75 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ARG B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.549A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 153
      removed outlier: 3.797A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   ILE B 169 " --> pdb=" O   PHE B 183 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE B 183 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL B 171 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.654A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 208 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   CYS B 226 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG B 222 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.995A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU B 261 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   LEU B 280 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 292 through 298
      removed outlier: 3.757A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 138
      removed outlier: 6.446A  pdb=" N   ILE A 103 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU A 137 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLY A 105 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   MET A 157 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA A  81 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY A 192 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    396 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1583
        1.34 -     1.45: 1447
        1.45 -     1.57: 2836
        1.57 -     1.69: 128
        1.69 -     1.81: 32
  Bond restraints: 6026
  Sorted by residual:
  bond pdb=" C2  SAM A 301 "
       pdb=" N3  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.322  1.381 -0.059 2.00e-02 2.50e+03 8.71e+00
  bond pdb=" C8  SAM A 301 "
       pdb=" N7  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.298  1.351 -0.053 2.00e-02 2.50e+03 7.13e+00
  bond pdb=" C2  SAM A 301 "
       pdb=" N1  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.329  1.380 -0.051 2.00e-02 2.50e+03 6.58e+00
  bond pdb=" C6  SAM A 301 "
       pdb=" N1  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.380 -0.043 2.00e-02 2.50e+03 4.57e+00
  bond pdb=" C   SAM A 301 "
       pdb=" OXT SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.256  1.230  0.026 2.00e-02 2.50e+03 1.64e+00
  ... (remaining 6021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 8218
        1.75 -     3.49: 223
        3.49 -     5.24: 40
        5.24 -     6.98: 3
        6.98 -     8.73: 3
  Bond angle restraints: 8487
  Sorted by residual:
  angle pdb=" O   SAM A 301 "
        pdb=" C   SAM A 301 "
        pdb=" OXT SAM A 301 "
      ideal   model   delta    sigma   weight residual
     126.77  118.04    8.73 3.00e+00 1.11e-01 8.47e+00
  angle pdb=" N1  SAM A 301 "
        pdb=" C2  SAM A 301 "
        pdb=" N3  SAM A 301 "
      ideal   model   delta    sigma   weight residual
     128.51  120.14    8.37 3.00e+00 1.11e-01 7.79e+00
  angle pdb=" C2  SAM A 301 "
        pdb=" N3  SAM A 301 "
        pdb=" C4  SAM A 301 "
      ideal   model   delta    sigma   weight residual
     112.25  120.28   -8.03 3.00e+00 1.11e-01 7.16e+00
  angle pdb=" C3'   A C   9 "
        pdb=" C2'   A C   9 "
        pdb=" O2'   A C   9 "
      ideal   model   delta    sigma   weight residual
     109.80  114.69   -4.89 2.00e+00 2.50e-01 5.99e+00
  angle pdb=" C3'   A C  58 "
        pdb=" C2'   A C  58 "
        pdb=" O2'   A C  58 "
      ideal   model   delta    sigma   weight residual
     109.80  114.64   -4.84 2.00e+00 2.50e-01 5.85e+00
  ... (remaining 8482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.44: 3063
       14.44 -    28.87: 179
       28.87 -    43.31: 68
       43.31 -    57.75: 56
       57.75 -    72.18: 35
  Dihedral angle restraints: 3401
    sinusoidal: 1806
      harmonic: 1595
  Sorted by residual:
  dihedral pdb=" C4'   A C  58 "
           pdb=" C3'   A C  58 "
           pdb=" C2'   A C  58 "
           pdb=" C1'   A C  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -35.84   72.18     1      3.10e+00 1.04e-01 6.93e+02
  dihedral pdb=" C4'   U C  20 "
           pdb=" C3'   U C  20 "
           pdb=" C2'   U C  20 "
           pdb=" C1'   U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.82   72.17     1      3.10e+00 1.04e-01 6.93e+02
  dihedral pdb=" C4'   G C  18 "
           pdb=" C3'   G C  18 "
           pdb=" C2'   G C  18 "
           pdb=" C1'   G C  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.47   71.82     1      3.10e+00 1.04e-01 6.87e+02
  ... (remaining 3398 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 822
       0.056 -    0.113: 85
       0.113 -    0.169: 9
       0.169 -    0.226: 4
       0.226 -    0.282: 82
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" C2'   A C   7 "
            pdb=" C3'   A C   7 "
            pdb=" O2'   A C   7 "
            pdb=" C1'   A C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.51   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C2'   G C  19 "
            pdb=" C3'   G C  19 "
            pdb=" O2'   G C  19 "
            pdb=" C1'   G C  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.51   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" C2'   U C  47 "
            pdb=" C3'   U C  47 "
            pdb=" O2'   U C  47 "
            pdb=" C1'   U C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.51   -0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 999 not shown)

  Planarity restraints: 837
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  59 "   -0.019 2.00e-02 2.50e+03   8.07e-03 1.96e+00
        pdb=" N9    G C  59 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    G C  59 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  59 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G C  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  59 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G C  59 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 318 "   -0.013 5.00e-02 4.00e+02   1.96e-02 6.14e-01
        pdb=" N   PRO B 319 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 154 "    0.012 5.00e-02 4.00e+02   1.88e-02 5.67e-01
        pdb=" N   PRO B 155 "   -0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO B 155 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 155 "    0.011 5.00e-02 4.00e+02
  ... (remaining 834 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1163
        2.78 -     3.31: 5195
        3.31 -     3.84: 10263
        3.84 -     4.37: 11749
        4.37 -     4.90: 18418
  Nonbonded interactions: 46788
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 154 "
            pdb=" OD1 ASP B 156 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR B 188 "
            pdb=" OE1 GLU B 189 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER B 130 "
            pdb=" OE1 GLU B 133 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O6    G C  10 "
            pdb=" N2    G C  45 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" OD2 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.307 3.040
  ... (remaining 46783 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
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:             0.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.870
  Find NCS groups from input model:        0.030
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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      :  0.002   0.059   6026  Z= 0.120
  Angle     :  0.642   8.728   8487  Z= 0.268
  Chirality :  0.078   0.282   1002
  Planarity :  0.002   0.020    837
  Dihedral  : 14.447  72.183   2369
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.21 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.09 (0.38), residues: 541
  helix:  1.26 (0.58), residues: 101
  sheet:  1.53 (0.39), residues: 183
  loop : -0.04 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  99 
 TYR   0.005   0.001   TYR A  37 
 PHE   0.010   0.001   PHE B  88 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.002   0.000   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.12 ( 6026)
  covalent geometry    : angle       0.64154 /  0.27 ( 8487)
  hydrogen bonds       : bond        0.12846 /  8.26 (  212)
  hydrogen bonds       : angle       4.53104 /  3.04 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9286 (pttt) cc_final: 0.8970 (mtmm)
REVERT: B  147 MET cc_start: 0.8776 (mtp) cc_final: 0.8398 (mtt)
REVERT: B  157 ASP cc_start: 0.9117 (t0) cc_final: 0.8817 (t0)
REVERT: B  166 ASP cc_start: 0.8776 (m-30) cc_final: 0.8424 (m-30)
REVERT: B  195 SER cc_start: 0.9390 (t) cc_final: 0.8737 (m)
REVERT: B  206 SER cc_start: 0.8836 (m) cc_final: 0.8560 (p)
REVERT: A   44 MET cc_start: 0.5281 (tmm) cc_final: 0.3599 (tmm)
REVERT: A  115 TYR cc_start: 0.9514 (t80) cc_final: 0.8864 (t80)
REVERT: A  140 ASN cc_start: 0.9171 (t0) cc_final: 0.8938 (t0)
REVERT: A  157 MET cc_start: 0.9333 (ttm) cc_final: 0.8863 (ttm)
REVERT: A  176 ILE cc_start: 0.9329 (mm) cc_final: 0.9039 (tp)
REVERT: A  180 LEU cc_start: 0.9654 (mt) cc_final: 0.9402 (mm)
REVERT: A  183 GLU cc_start: 0.9262 (pt0) cc_final: 0.8847 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 65
  average time/residue: 0.0965
  time to fit residues: 7.9382
Evaluate side-chains
  43 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   overall best weight:    5.7590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.038534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.029179 restraints weight = 48275.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.030307 restraints weight = 24696.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.031085 restraints weight = 15995.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.031627 restraints weight = 11788.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.031965 restraints weight = 9456.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (16 function evaluations)
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   6026  Z= 0.273
  Angle     :  0.920  12.800   8487  Z= 0.393
  Chirality :  0.065   0.542   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 15.026 153.681   1370
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.37), residues: 541
  helix:  1.41 (0.58), residues: 97
  sheet:  1.17 (0.38), residues: 186
  loop : -0.08 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  99 
 TYR   0.013   0.002   TYR B 127 
 PHE   0.024   0.002   PHE B 297 
 TRP   0.015   0.002   TRP B  93 
 HIS   0.004   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00558 /  0.27 ( 6026)
  covalent geometry    : angle       0.91986 /  0.39 ( 8487)
  hydrogen bonds       : bond        0.07980 /  5.23 (  212)
  hydrogen bonds       : angle       4.22807 /  2.83 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9383 (pttt) cc_final: 0.9001 (mtmm)
REVERT: A   27 SER cc_start: 0.9603 (m) cc_final: 0.9248 (t)
REVERT: A   44 MET cc_start: 0.6313 (tmm) cc_final: 0.5051 (tmm)
REVERT: A  115 TYR cc_start: 0.9588 (t80) cc_final: 0.9204 (t80)
REVERT: A  157 MET cc_start: 0.9337 (ttm) cc_final: 0.8801 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0970
  time to fit residues: 5.1085
Evaluate side-chains
  32 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 272 GLN
B 279 GLN
B 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.036399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.027207 restraints weight = 49324.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.028249 restraints weight = 25512.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.028976 restraints weight = 16730.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.029502 restraints weight = 12338.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.029864 restraints weight = 9930.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (15 function evaluations)
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6026  Z= 0.228
  Angle     :  0.794   7.736   8487  Z= 0.352
  Chirality :  0.059   0.438   1002
  Planarity :  0.003   0.037    837
  Dihedral  : 15.539 160.861   1370
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.55 (0.36), residues: 541
  helix:  1.53 (0.58), residues: 91
  sheet:  0.83 (0.39), residues: 172
  loop : -0.29 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  99 
 TYR   0.010   0.002   TYR B 127 
 PHE   0.018   0.002   PHE B  69 
 TRP   0.015   0.002   TRP B  93 
 HIS   0.004   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.23 ( 6026)
  covalent geometry    : angle       0.79421 /  0.35 ( 8487)
  hydrogen bonds       : bond        0.06178 /  4.23 (  212)
  hydrogen bonds       : angle       4.24172 /  2.81 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: B  166 ASP cc_start: 0.9119 (m-30) cc_final: 0.8916 (m-30)
REVERT: B  168 LYS cc_start: 0.9119 (mttm) cc_final: 0.8797 (mmmm)
REVERT: A   27 SER cc_start: 0.9628 (m) cc_final: 0.9335 (t)
REVERT: A   44 MET cc_start: 0.6761 (tmm) cc_final: 0.5749 (tmm)
REVERT: A  115 TYR cc_start: 0.9601 (t80) cc_final: 0.9108 (t80)
REVERT: A  157 MET cc_start: 0.9277 (ttm) cc_final: 0.8977 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0837
  time to fit residues: 4.0058
Evaluate side-chains
  27 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 37 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    4.2188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.036372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.027130 restraints weight = 49029.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.028178 restraints weight = 25439.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.028930 restraints weight = 16674.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.029453 restraints weight = 12225.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.029812 restraints weight = 9855.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6026  Z= 0.194
  Angle     :  0.738   7.874   8487  Z= 0.326
  Chirality :  0.054   0.353   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 15.586 176.316   1370
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.50 (0.37), residues: 541
  helix:  1.59 (0.56), residues: 91
  sheet:  0.76 (0.37), residues: 184
  loop : -0.37 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.007   0.001   TYR A  50 
 PHE   0.018   0.002   PHE B  88 
 TRP   0.014   0.001   TRP B  93 
 HIS   0.007   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.19 ( 6026)
  covalent geometry    : angle       0.73808 /  0.33 ( 8487)
  hydrogen bonds       : bond        0.05933 /  3.94 (  212)
  hydrogen bonds       : angle       4.21928 /  2.84 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: B  166 ASP cc_start: 0.9312 (m-30) cc_final: 0.9039 (m-30)
REVERT: B  168 LYS cc_start: 0.9104 (mttm) cc_final: 0.8755 (mmmm)
REVERT: A   27 SER cc_start: 0.9615 (m) cc_final: 0.9333 (t)
REVERT: A   44 MET cc_start: 0.7001 (tmm) cc_final: 0.6095 (tmm)
REVERT: A  115 TYR cc_start: 0.9602 (t80) cc_final: 0.9039 (t80)
REVERT: A  157 MET cc_start: 0.9243 (ttm) cc_final: 0.8917 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0771
  time to fit residues: 3.7829
Evaluate side-chains
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 57 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    3.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.036616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.027421 restraints weight = 50430.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.028488 restraints weight = 25945.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.029185 restraints weight = 16931.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.029770 restraints weight = 12652.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.030102 restraints weight = 10061.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (11 function evaluations)
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6026  Z= 0.180
  Angle     :  0.726   8.020   8487  Z= 0.319
  Chirality :  0.054   0.316   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 15.527 174.080   1370
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.52 (0.37), residues: 541
  helix:  1.63 (0.56), residues: 91
  sheet:  0.76 (0.38), residues: 184
  loop : -0.36 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.008   0.001   TYR A  50 
 PHE   0.014   0.002   PHE B  88 
 TRP   0.013   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.18 ( 6026)
  covalent geometry    : angle       0.72567 /  0.32 ( 8487)
  hydrogen bonds       : bond        0.05554 /  3.69 (  212)
  hydrogen bonds       : angle       4.21028 /  2.84 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9556 (mt) cc_final: 0.9335 (mt)
REVERT: B  166 ASP cc_start: 0.9410 (m-30) cc_final: 0.9144 (m-30)
REVERT: B  168 LYS cc_start: 0.9112 (mttm) cc_final: 0.8754 (mmmm)
REVERT: A   27 SER cc_start: 0.9665 (m) cc_final: 0.9396 (t)
REVERT: A   44 MET cc_start: 0.7042 (tmm) cc_final: 0.6168 (tmm)
REVERT: A  115 TYR cc_start: 0.9596 (t80) cc_final: 0.9028 (t80)
REVERT: A  142 MET cc_start: 0.9698 (mmm) cc_final: 0.9492 (mmm)
REVERT: A  157 MET cc_start: 0.9258 (ttm) cc_final: 0.8943 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0740
  time to fit residues: 3.5748
Evaluate side-chains
  30 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0670
   chunk 34 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    3.8126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.036711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.027592 restraints weight = 50191.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.028655 restraints weight = 25911.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.029395 restraints weight = 16903.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.029928 restraints weight = 12439.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.030306 restraints weight = 9980.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6026  Z= 0.177
  Angle     :  0.728   8.607   8487  Z= 0.320
  Chirality :  0.053   0.294   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 15.503 171.036   1370
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.48 (0.37), residues: 541
  helix:  1.67 (0.57), residues: 91
  sheet:  0.79 (0.38), residues: 182
  loop : -0.46 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.007   0.001   TYR A  50 
 PHE   0.015   0.001   PHE B  88 
 TRP   0.015   0.002   TRP A 206 
 HIS   0.007   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.18 ( 6026)
  covalent geometry    : angle       0.72802 /  0.32 ( 8487)
  hydrogen bonds       : bond        0.05315 /  3.55 (  212)
  hydrogen bonds       : angle       4.16301 /  2.81 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 ASP cc_start: 0.9488 (m-30) cc_final: 0.9232 (m-30)
REVERT: B  168 LYS cc_start: 0.8985 (mttm) cc_final: 0.8671 (mmmm)
REVERT: A   27 SER cc_start: 0.9662 (m) cc_final: 0.9400 (t)
REVERT: A   44 MET cc_start: 0.7150 (tmm) cc_final: 0.6260 (tmm)
REVERT: A  115 TYR cc_start: 0.9595 (t80) cc_final: 0.9024 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0752
  time to fit residues: 3.4640
Evaluate side-chains
  31 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.0010
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    5.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.035594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2530 r_free = 0.2530 target = 0.026632 restraints weight = 50666.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.027665 restraints weight = 26115.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.028362 restraints weight = 16991.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.028884 restraints weight = 12654.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.029250 restraints weight = 10134.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6026  Z= 0.238
  Angle     :  0.796   9.354   8487  Z= 0.353
  Chirality :  0.054   0.297   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 15.487 169.127   1370
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.26 (0.36), residues: 541
  helix:  1.51 (0.55), residues: 91
  sheet:  0.53 (0.38), residues: 184
  loop : -0.52 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 170 
 TYR   0.015   0.002   TYR A 186 
 PHE   0.021   0.002   PHE B 297 
 TRP   0.016   0.002   TRP A 206 
 HIS   0.007   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.24 ( 6026)
  covalent geometry    : angle       0.79601 /  0.35 ( 8487)
  hydrogen bonds       : bond        0.06184 /  4.12 (  212)
  hydrogen bonds       : angle       4.51405 /  3.08 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9532 (mt) cc_final: 0.9267 (mt)
REVERT: B  168 LYS cc_start: 0.8985 (mttm) cc_final: 0.8783 (mmmm)
REVERT: A   27 SER cc_start: 0.9635 (m) cc_final: 0.9363 (t)
REVERT: A   44 MET cc_start: 0.7420 (tmm) cc_final: 0.6838 (tmm)
REVERT: A  115 TYR cc_start: 0.9576 (t80) cc_final: 0.9007 (t80)
REVERT: A  142 MET cc_start: 0.9528 (mmm) cc_final: 0.9295 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0858
  time to fit residues: 3.9793
Evaluate side-chains
  28 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.036685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.027612 restraints weight = 48911.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.028665 restraints weight = 25285.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.029418 restraints weight = 16550.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.029951 restraints weight = 12197.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.030327 restraints weight = 9770.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6026  Z= 0.162
  Angle     :  0.732   8.920   8487  Z= 0.321
  Chirality :  0.053   0.289   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 15.287 171.150   1370
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.36), residues: 541
  helix:  1.58 (0.56), residues: 91
  sheet:  0.74 (0.38), residues: 181
  loop : -0.46 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.012   0.001   TYR A 186 
 PHE   0.013   0.001   PHE B  88 
 TRP   0.017   0.001   TRP A 206 
 HIS   0.010   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.16 ( 6026)
  covalent geometry    : angle       0.73158 /  0.32 ( 8487)
  hydrogen bonds       : bond        0.04840 /  3.20 (  212)
  hydrogen bonds       : angle       4.18800 /  2.82 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9011 (mtm) cc_final: 0.8557 (mtm)
REVERT: B  148 LEU cc_start: 0.9650 (mt) cc_final: 0.9379 (mt)
REVERT: B  168 LYS cc_start: 0.8953 (mttm) cc_final: 0.8720 (mmmm)
REVERT: B  361 TYR cc_start: 0.8593 (m-80) cc_final: 0.8303 (m-10)
REVERT: A   27 SER cc_start: 0.9611 (m) cc_final: 0.9304 (t)
REVERT: A   44 MET cc_start: 0.7307 (tmm) cc_final: 0.6750 (tmm)
REVERT: A  115 TYR cc_start: 0.9602 (t80) cc_final: 0.9017 (t80)
REVERT: A  142 MET cc_start: 0.9499 (mmm) cc_final: 0.9230 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0745
  time to fit residues: 4.0550
Evaluate side-chains
  30 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.035760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.026892 restraints weight = 51336.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2579 r_free = 0.2579 target = 0.027910 restraints weight = 26615.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.028616 restraints weight = 17492.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.029087 restraints weight = 12964.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.029480 restraints weight = 10563.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6026  Z= 0.215
  Angle     :  0.769   8.850   8487  Z= 0.341
  Chirality :  0.053   0.285   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 15.272 169.553   1370
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.36), residues: 541
  helix:  1.47 (0.56), residues: 91
  sheet:  0.55 (0.39), residues: 174
  loop : -0.46 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  99 
 TYR   0.010   0.002   TYR B 361 
 PHE   0.017   0.002   PHE B  88 
 TRP   0.018   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.22 ( 6026)
  covalent geometry    : angle       0.76898 /  0.34 ( 8487)
  hydrogen bonds       : bond        0.05547 /  3.70 (  212)
  hydrogen bonds       : angle       4.36688 /  2.97 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8989 (mtm) cc_final: 0.8495 (mtm)
REVERT: B  148 LEU cc_start: 0.9644 (mt) cc_final: 0.9361 (mt)
REVERT: A   27 SER cc_start: 0.9612 (m) cc_final: 0.9363 (t)
REVERT: A   44 MET cc_start: 0.7399 (tmm) cc_final: 0.6777 (tmm)
REVERT: A  115 TYR cc_start: 0.9562 (t80) cc_final: 0.8982 (t80)
REVERT: A  142 MET cc_start: 0.9534 (mmm) cc_final: 0.9277 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0750
  time to fit residues: 3.4918
Evaluate side-chains
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0970
   chunk 48 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    3.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.036202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.027136 restraints weight = 50846.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.028195 restraints weight = 26292.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.028887 restraints weight = 17106.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.029422 restraints weight = 12711.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.029692 restraints weight = 10184.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6026  Z= 0.178
  Angle     :  0.734   7.845   8487  Z= 0.325
  Chirality :  0.052   0.296   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 15.242 171.261   1370
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.31 (0.37), residues: 541
  helix:  1.49 (0.56), residues: 91
  sheet:  0.63 (0.39), residues: 175
  loop : -0.48 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 170 
 TYR   0.009   0.001   TYR A 186 
 PHE   0.019   0.002   PHE B  88 
 TRP   0.019   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.18 ( 6026)
  covalent geometry    : angle       0.73352 /  0.33 ( 8487)
  hydrogen bonds       : bond        0.04925 /  3.30 (  212)
  hydrogen bonds       : angle       4.27896 /  2.90 (  510)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  148 LEU cc_start: 0.9670 (mt) cc_final: 0.9401 (mt)
REVERT: A   27 SER cc_start: 0.9593 (m) cc_final: 0.9350 (t)
REVERT: A   44 MET cc_start: 0.7329 (tmm) cc_final: 0.6733 (tmm)
REVERT: A  115 TYR cc_start: 0.9564 (t80) cc_final: 0.8976 (t80)
REVERT: A  142 MET cc_start: 0.9505 (mmm) cc_final: 0.9241 (mmm)
REVERT: A  184 TYR cc_start: 0.9187 (m-80) cc_final: 0.8818 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0742
  time to fit residues: 3.4333
Evaluate side-chains
  30 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0470
   chunk 36 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    1.8282

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.037680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.028380 restraints weight = 48055.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.029464 restraints weight = 24941.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.030197 restraints weight = 16295.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.030725 restraints weight = 12094.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.031102 restraints weight = 9769.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.5087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6026  Z= 0.119
  Angle     :  0.702   7.256   8487  Z= 0.309
  Chirality :  0.052   0.292   1002
  Planarity :  0.003   0.025    837
  Dihedral  : 15.166 174.535   1370
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.47 (0.37), residues: 541
  helix:  1.45 (0.56), residues: 91
  sheet:  0.84 (0.39), residues: 180
  loop : -0.42 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.011   0.001   TYR A 186 
 PHE   0.018   0.001   PHE B  88 
 TRP   0.019   0.001   TRP A 206 
 HIS   0.007   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 ( 6026)
  covalent geometry    : angle       0.70245 /  0.31 ( 8487)
  hydrogen bonds       : bond        0.04209 /  2.87 (  212)
  hydrogen bonds       : angle       4.02348 /  2.71 (  510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 921.64 seconds
wall clock time: 16 minutes 42.07 seconds (1002.07 seconds total)