Starting phenix.real_space_refine
on Sat Apr  4 21:51:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9odp_70372/04_2026/9odp_70372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9odp_70372/04_2026/9odp_70372.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9odp_70372/04_2026/9odp_70372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9odp_70372/04_2026/9odp_70372.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9odp_70372/04_2026/9odp_70372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9odp_70372/04_2026/9odp_70372.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S       7      5.16       5
     C    2672      2.51       5
     N     783      2.21       5
     O     782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4248
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 1934
          Classifications: {'peptide': 335}
          Incomplete info: {'truncation_to_alanine': 236}
          Link IDs: {'PTRANS': 4, 'TRANS': 330}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 770
          Unresolved non-hydrogen angles: 955
          Unresolved non-hydrogen dihedrals: 602
          Unresolved non-hydrogen chiralities: 78
          Planarities with less than four sites: {'GLU:plan': 26, 'ASP:plan': 24, 'ARG:plan': 16, 'ASN:plan1': 11, 'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 1, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 386
    Chain: "B"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 1993
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 197}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 594
          Unresolved non-hydrogen angles: 751
          Unresolved non-hydrogen dihedrals: 444
          Unresolved non-hydrogen chiralities: 70
          Planarities with less than four sites: {'ASP:plan': 28, 'GLN:plan1': 11, 'ARG:plan': 19, 'GLU:plan': 8, 'ASN:plan1': 13, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 315
    Chain: "G"
      Number of atoms: 288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 288
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 64
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.06, per 1000 atoms: 0.25
  Number of scatterers: 4248
  At special positions: 0
  Unit cell: (74.6222, 92.8439, 94.5793, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       7     16.00
     P       3     15.00
     Mg      1     11.99
     O     782      8.00
     N     783      7.00
     C    2672      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: 0.43
  Conformation dependent library (CDL) restraints added in 382.6 milliseconds
  

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 8 sheets defined
      35.8% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 31
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 62 through 91
    Processing helix  chain 'A' and resid 99 through 111
      removed outlier: 3.869A  pdb=" N   VAL A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 133
    Processing helix  chain 'A' and resid 133 through 142
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
      removed outlier: 3.962A  pdb=" N   ARG A 176 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 3.714A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.574A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 262
      removed outlier: 4.503A  pdb=" N   ASP A 261 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 262 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.704A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.539A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 346
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 5.275A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A  37 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 265 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.749A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.165A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 102
      removed outlier: 7.327A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.033A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.059A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 7.032A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.363A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    723 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.61

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1497
        1.34 -     1.46: 1098
        1.46 -     1.58: 1725
        1.58 -     1.69: 5
        1.69 -     1.81: 8
  Bond restraints: 4333
  Sorted by residual:
  bond pdb=" CB  ASN A 269 "
       pdb=" CG  ASN A 269 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" C   ILE A 168 "
       pdb=" O   ILE A 168 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.009 1.01e-02 9.80e+03 7.21e-01
  bond pdb=" C   GLY A 202 "
       pdb=" N   GLY A 203 "
    ideal  model  delta    sigma   weight residual
    1.333  1.325  0.008 1.10e-02 8.26e+03 5.37e-01
  bond pdb=" N   TYR A 287 "
       pdb=" CA  TYR A 287 "
    ideal  model  delta    sigma   weight residual
    1.462  1.455  0.007 1.07e-02 8.73e+03 4.77e-01
  bond pdb=" C   THR B 243 "
       pdb=" N   GLY B 244 "
    ideal  model  delta    sigma   weight residual
    1.322  1.331 -0.009 1.41e-02 5.03e+03 4.11e-01
  ... (remaining 4328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 5781
        1.17 -     2.34: 188
        2.34 -     3.51: 31
        3.51 -     4.68: 6
        4.68 -     5.85: 3
  Bond angle restraints: 6009
  Sorted by residual:
  angle pdb=" N   GLY B  77 "
        pdb=" CA  GLY B  77 "
        pdb=" C   GLY B  77 "
      ideal   model   delta    sigma   weight residual
     114.90  111.22    3.68 1.54e+00 4.22e-01 5.71e+00
  angle pdb=" N   ASN B 155 "
        pdb=" CA  ASN B 155 "
        pdb=" C   ASN B 155 "
      ideal   model   delta    sigma   weight residual
     114.12  110.93    3.19 1.39e+00 5.18e-01 5.26e+00
  angle pdb=" C   ILE A  49 "
        pdb=" CA  ILE A  49 "
        pdb=" CB  ILE A  49 "
      ideal   model   delta    sigma   weight residual
     112.16  108.96    3.20 1.55e+00 4.16e-01 4.26e+00
  angle pdb=" C2' GTP A 401 "
        pdb=" C3' GTP A 401 "
        pdb=" C4' GTP A 401 "
      ideal   model   delta    sigma   weight residual
     111.00  105.15    5.85 3.00e+00 1.11e-01 3.80e+00
  angle pdb=" N   ASP B 312 "
        pdb=" CA  ASP B 312 "
        pdb=" C   ASP B 312 "
      ideal   model   delta    sigma   weight residual
     113.88  111.58    2.30 1.23e+00 6.61e-01 3.50e+00
  ... (remaining 6004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.67: 2394
       34.67 -    69.35: 16
       69.35 -   104.02: 1
      104.02 -   138.69: 1
      138.69 -   173.36: 1
  Dihedral angle restraints: 2413
    sinusoidal: 310
      harmonic: 2103
  Sorted by residual:
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  100.76  173.36     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -17.62  122.21     1      2.00e+01 2.50e-03 3.68e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92 -169.80  100.88     1      2.00e+01 2.50e-03 2.85e+01
  ... (remaining 2410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 385
       0.025 -    0.050: 191
       0.050 -    0.074: 82
       0.074 -    0.099: 37
       0.099 -    0.124: 27
  Chirality restraints: 722
  Sorted by residual:
  chirality pdb=" CA  ILE B 229 "
            pdb=" N   ILE B 229 "
            pdb=" C   ILE B 229 "
            pdb=" CB  ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE B 157 "
            pdb=" N   ILE B 157 "
            pdb=" C   ILE B 157 "
            pdb=" CB  ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 719 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.017 5.00e-02 4.00e+02   2.63e-02 1.10e+00
        pdb=" N   PRO B 236 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  69 "    0.005 2.00e-02 2.50e+03   6.03e-03 7.27e-01
        pdb=" CG  TYR A  69 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  69 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  69 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  69 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  69 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  69 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 106 "   -0.013 5.00e-02 4.00e+02   2.01e-02 6.46e-01
        pdb=" N   PRO B 107 "    0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 20
        2.58 -     3.16: 3291
        3.16 -     3.74: 6329
        3.74 -     4.32: 7060
        4.32 -     4.90: 12203
  Nonbonded interactions: 28903
  Sorted by model distance:
  nonbonded pdb=" O2B GTP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     2.003 2.170
  nonbonded pdb=" O3G GTP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     2.109 2.170
  nonbonded pdb=" O3A GTP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     2.170 2.170
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ALA A  41 "
            pdb=" NZ  LYS A  46 "
     model   vdw
     2.291 3.120
  ... (remaining 28898 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.060
  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:                    0.020
  Process input model:                     5.990
  Find NCS groups from input model:        0.040
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
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   0.026   4333  Z= 0.117
  Angle     :  0.532   5.849   6009  Z= 0.322
  Chirality :  0.042   0.124    722
  Planarity :  0.002   0.026    813
  Dihedral  : 11.848 173.362   1049
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.33), residues: 714
  helix:  2.79 (0.35), residues: 248
  sheet: -1.08 (0.41), residues: 158
  loop : -1.24 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.007   0.001   PHE A 307 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 4333)
  covalent geometry    : angle       0.53213 ( 6009)
  hydrogen bonds       : bond        0.15572 (  248)
  hydrogen bonds       : angle       5.55435 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.8829 (m-80) cc_final: 0.8527 (m-80)
REVERT: B  124 TYR cc_start: 0.7286 (m-80) cc_final: 0.7082 (m-80)
REVERT: B  142 HIS cc_start: 0.6154 (m-70) cc_final: 0.5870 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0617
  time to fit residues: 4.6838
Evaluate side-chains
  45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0270
   chunk 33 optimal weight:   40.0000
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    4.9644

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.060385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.048608 restraints weight = 30761.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.049556 restraints weight = 21893.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.050069 restraints weight = 16913.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.050703 restraints weight = 14371.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.050875 restraints weight = 12518.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4333  Z= 0.255
  Angle     :  0.603   6.761   6009  Z= 0.343
  Chirality :  0.044   0.170    722
  Planarity :  0.004   0.033    813
  Dihedral  : 10.091 163.216    759
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.33), residues: 714
  helix:  2.72 (0.33), residues: 255
  sheet: -1.25 (0.38), residues: 172
  loop : -1.29 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  48 
 TYR   0.016   0.002   TYR A  69 
 PHE   0.020   0.003   PHE B 234 
 TRP   0.026   0.003   TRP A 258 
 HIS   0.010   0.002   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 4333)
  covalent geometry    : angle       0.60291 ( 6009)
  hydrogen bonds       : bond        0.04120 (  248)
  hydrogen bonds       : angle       4.70412 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9141 (m-80) cc_final: 0.8672 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0308
  time to fit residues: 2.1202
Evaluate side-chains
  33 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 46 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 2 optimal weight:   20.0000
   chunk 1 optimal weight:   30.0000
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.062727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.050937 restraints weight = 29215.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.051923 restraints weight = 20419.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.052596 restraints weight = 15751.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.053183 restraints weight = 13121.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.053403 restraints weight = 11439.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4333  Z= 0.103
  Angle     :  0.433   6.354   6009  Z= 0.236
  Chirality :  0.042   0.131    722
  Planarity :  0.003   0.038    813
  Dihedral  :  9.585 153.123    759
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.34), residues: 714
  helix:  3.21 (0.33), residues: 255
  sheet: -1.50 (0.37), residues: 172
  loop : -1.20 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.010   0.001   TYR B  85 
 PHE   0.007   0.001   PHE B 235 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 4333)
  covalent geometry    : angle       0.43289 ( 6009)
  hydrogen bonds       : bond        0.02784 (  248)
  hydrogen bonds       : angle       3.84664 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.8968 (m-80) cc_final: 0.8540 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0309
  time to fit residues: 2.2445
Evaluate side-chains
  34 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:   30.0000
   chunk 18 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:   20.0000
   chunk 6 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 0 optimal weight:   40.0000
   overall best weight:    5.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.058315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.046491 restraints weight = 31114.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.047408 restraints weight = 21718.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.048077 restraints weight = 16870.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.048569 restraints weight = 14037.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.048782 restraints weight = 12285.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   4333  Z= 0.279
  Angle     :  0.632   8.048   6009  Z= 0.357
  Chirality :  0.045   0.137    722
  Planarity :  0.004   0.042    813
  Dihedral  : 10.248 138.996    759
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.33), residues: 714
  helix:  2.57 (0.32), residues: 255
  sheet: -1.81 (0.38), residues: 176
  loop : -1.44 (0.38), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  48 
 TYR   0.018   0.003   TYR A 230 
 PHE   0.033   0.003   PHE B 234 
 TRP   0.025   0.003   TRP B 297 
 HIS   0.007   0.003   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 4333)
  covalent geometry    : angle       0.63247 ( 6009)
  hydrogen bonds       : bond        0.04291 (  248)
  hydrogen bonds       : angle       4.85853 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9192 (m-80) cc_final: 0.8766 (m-80)
REVERT: B   49 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7335 (mtp180)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0371
  time to fit residues: 1.9915
Evaluate side-chains
  32 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 28 optimal weight:   30.0000
   chunk 59 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 44 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:   30.0000
   overall best weight:    2.3188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.060990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.049304 restraints weight = 29696.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.050293 restraints weight = 20690.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.050982 restraints weight = 15976.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.051513 restraints weight = 13219.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.051840 restraints weight = 11525.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4333  Z= 0.123
  Angle     :  0.459   6.924   6009  Z= 0.253
  Chirality :  0.042   0.137    722
  Planarity :  0.003   0.044    813
  Dihedral  :  9.464 141.186    759
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.34), residues: 714
  helix:  3.25 (0.32), residues: 255
  sheet: -1.64 (0.39), residues: 176
  loop : -1.41 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  48 
 TYR   0.009   0.001   TYR A 320 
 PHE   0.013   0.001   PHE B 234 
 TRP   0.017   0.002   TRP B 332 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4333)
  covalent geometry    : angle       0.45863 ( 6009)
  hydrogen bonds       : bond        0.02977 (  248)
  hydrogen bonds       : angle       3.99590 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9062 (m-80) cc_final: 0.8658 (m-80)
REVERT: B   49 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7259 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0445
  time to fit residues: 2.3617
Evaluate side-chains
  30 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:   40.0000
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.060405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.048398 restraints weight = 30570.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.049378 restraints weight = 20802.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.050152 restraints weight = 15935.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.050712 restraints weight = 13117.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.051029 restraints weight = 11359.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4333  Z= 0.156
  Angle     :  0.481   7.241   6009  Z= 0.266
  Chirality :  0.042   0.132    722
  Planarity :  0.003   0.040    813
  Dihedral  :  9.153 129.109    759
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.34), residues: 714
  helix:  3.28 (0.32), residues: 255
  sheet: -1.53 (0.40), residues: 175
  loop : -1.49 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.010   0.001   TYR A 230 
 PHE   0.017   0.002   PHE B 234 
 TRP   0.024   0.002   TRP B 332 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4333)
  covalent geometry    : angle       0.48051 ( 6009)
  hydrogen bonds       : bond        0.03188 (  248)
  hydrogen bonds       : angle       4.04166 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9110 (m-80) cc_final: 0.8665 (m-80)
REVERT: B   49 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7290 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0444
  time to fit residues: 2.4069
Evaluate side-chains
  30 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 2 optimal weight:   30.0000
   chunk 23 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:   40.0000
   chunk 53 optimal weight:   20.0000
   chunk 59 optimal weight:    0.0060
   chunk 11 optimal weight:   50.0000
   chunk 51 optimal weight:    9.9990
   overall best weight:    3.7202

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.059526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.047798 restraints weight = 30627.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.048803 restraints weight = 20940.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.049530 restraints weight = 15974.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.049935 restraints weight = 13180.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.050374 restraints weight = 11588.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.5649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4333  Z= 0.184
  Angle     :  0.515   7.461   6009  Z= 0.283
  Chirality :  0.043   0.132    722
  Planarity :  0.003   0.042    813
  Dihedral  :  9.110 125.724    759
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.34), residues: 714
  helix:  3.16 (0.32), residues: 255
  sheet: -1.55 (0.40), residues: 175
  loop : -1.55 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.013   0.002   TYR A 320 
 PHE   0.020   0.002   PHE B 234 
 TRP   0.020   0.002   TRP B 332 
 HIS   0.005   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4333)
  covalent geometry    : angle       0.51490 ( 6009)
  hydrogen bonds       : bond        0.03421 (  248)
  hydrogen bonds       : angle       4.23017 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9109 (m-80) cc_final: 0.8689 (m-80)
REVERT: B   49 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7326 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0344
  time to fit residues: 1.8728
Evaluate side-chains
  30 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 33 optimal weight:   40.0000
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.058987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.047214 restraints weight = 30668.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.048188 restraints weight = 21239.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.048889 restraints weight = 16333.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.049367 restraints weight = 13469.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.049772 restraints weight = 11824.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.5861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4333  Z= 0.205
  Angle     :  0.548   7.535   6009  Z= 0.304
  Chirality :  0.043   0.157    722
  Planarity :  0.003   0.042    813
  Dihedral  :  9.251 131.293    759
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.34), residues: 714
  helix:  3.07 (0.32), residues: 255
  sheet: -1.66 (0.39), residues: 175
  loop : -1.63 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.013   0.002   TYR A 320 
 PHE   0.023   0.002   PHE B 234 
 TRP   0.018   0.002   TRP B 332 
 HIS   0.008   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4333)
  covalent geometry    : angle       0.54846 ( 6009)
  hydrogen bonds       : bond        0.03585 (  248)
  hydrogen bonds       : angle       4.36001 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9135 (m-80) cc_final: 0.8711 (m-80)
REVERT: B   49 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7376 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0366
  time to fit residues: 1.9290
Evaluate side-chains
  32 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:   10.0000
   chunk 21 optimal weight:    0.0970
   chunk 54 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 60 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.060775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.048767 restraints weight = 30165.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.049805 restraints weight = 20457.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.050583 restraints weight = 15469.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.051150 restraints weight = 12647.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.051432 restraints weight = 10935.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4333  Z= 0.102
  Angle     :  0.458   6.788   6009  Z= 0.246
  Chirality :  0.042   0.146    722
  Planarity :  0.003   0.041    813
  Dihedral  :  8.865 127.731    759
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.34), residues: 714
  helix:  3.45 (0.33), residues: 249
  sheet: -1.39 (0.40), residues: 167
  loop : -1.44 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  22 
 TYR   0.009   0.001   TYR A 320 
 PHE   0.011   0.001   PHE A 307 
 TRP   0.011   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 4333)
  covalent geometry    : angle       0.45774 ( 6009)
  hydrogen bonds       : bond        0.02747 (  248)
  hydrogen bonds       : angle       3.85783 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9056 (m-80) cc_final: 0.8617 (m-80)
REVERT: B   49 ARG cc_start: 0.7774 (ttm170) cc_final: 0.7322 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0359
  time to fit residues: 2.1565
Evaluate side-chains
  33 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 9 optimal weight:   40.0000
   chunk 42 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0010
   chunk 36 optimal weight:    0.4980
   chunk 68 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.6590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.061042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.049096 restraints weight = 29916.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.050142 restraints weight = 20182.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.050940 restraints weight = 15225.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.051486 restraints weight = 12406.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.051948 restraints weight = 10733.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.5802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4333  Z= 0.097
  Angle     :  0.448   6.676   6009  Z= 0.239
  Chirality :  0.042   0.141    722
  Planarity :  0.002   0.039    813
  Dihedral  :  8.685 129.857    759
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.35), residues: 714
  helix:  3.45 (0.34), residues: 252
  sheet: -1.42 (0.40), residues: 172
  loop : -1.38 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 234 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 4333)
  covalent geometry    : angle       0.44765 ( 6009)
  hydrogen bonds       : bond        0.02611 (  248)
  hydrogen bonds       : angle       3.69998 (  723)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9064 (m-80) cc_final: 0.8602 (m-80)
REVERT: B   49 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7228 (mtt180)
REVERT: B  124 TYR cc_start: 0.8345 (m-80) cc_final: 0.8003 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0387
  time to fit residues: 2.1226
Evaluate side-chains
  35 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.057730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.046087 restraints weight = 30950.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.047020 restraints weight = 21349.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.047681 restraints weight = 16507.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.048176 restraints weight = 13721.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.048425 restraints weight = 12029.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.6272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   4333  Z= 0.300
  Angle     :  0.641   8.777   6009  Z= 0.360
  Chirality :  0.045   0.144    722
  Planarity :  0.004   0.042    813
  Dihedral  :  9.317 140.024    759
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.33), residues: 714
  helix:  2.78 (0.32), residues: 254
  sheet: -1.56 (0.40), residues: 170
  loop : -1.81 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.017   0.002   TYR A 230 
 PHE   0.032   0.003   PHE B 234 
 TRP   0.022   0.003   TRP B  99 
 HIS   0.008   0.003   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 4333)
  covalent geometry    : angle       0.64111 ( 6009)
  hydrogen bonds       : bond        0.04186 (  248)
  hydrogen bonds       : angle       4.69231 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 738.70 seconds
wall clock time: 13 minutes 16.80 seconds (796.80 seconds total)