Starting phenix.real_space_refine
on Wed Sep 17 08:33:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6i2i_0331/09_2025/6i2i_0331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6i2i_0331/09_2025/6i2i_0331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2025/6i2i_0331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2025/6i2i_0331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2025/6i2i_0331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2025/6i2i_0331.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.016
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       6      5.49       5
     Mg      2      5.21       5
     S      46      5.16       5
     C    4303      2.51       5
     N    1157      2.21       5
     O    1316      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6830
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3356
          Classifications: {'peptide': 430}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3346
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    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}
    Chain: "B"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 95
          Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.88, per 1000 atoms: 0.28
  Number of scatterers: 6830
  At special positions: 0
  Unit cell: (75.35, 71.24, 115.08, 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      46     16.00
     P       6     15.00
     Mg      2     11.99
     O    1316      8.00
     N    1157      7.00
     C    4303      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: 0.69
  Conformation dependent library (CDL) restraints added in 407.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 8 sheets defined
      47.0% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
      removed outlier: 3.648A  pdb=" N   ALA A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   CYS A  25 " --> pdb=" O   TRP A  21 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLY A  29 " --> pdb=" O   CYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
      removed outlier: 3.888A  pdb=" N   ASP A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 85
      removed outlier: 4.140A  pdb=" N   GLN A  85 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 85'
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.890A  pdb=" N   GLY A 106 " --> pdb=" O   ASN A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 127
      removed outlier: 4.222A  pdb=" N   ILE A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASP A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   LYS A 124 " --> pdb=" O   ASP A 120 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 4.280A  pdb=" N   GLY A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 144 through 149'
    Processing helix  chain 'A' and resid 149 through 161
      removed outlier: 4.048A  pdb=" N   GLU A 155 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   SER A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   VAL A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
      removed outlier: 3.595A  pdb=" N   SER A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ILE A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LEU A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   THR A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 194
    Processing helix  chain 'A' and resid 206 through 211
      removed outlier: 3.812A  pdb=" N   TYR A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 206 through 211'
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 223 through 228
    Processing helix  chain 'A' and resid 228 through 239
      removed outlier: 3.693A  pdb=" N   GLN A 233 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A 237 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE A 238 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 244
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 3.848A  pdb=" N   THR A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASN A 258 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 292
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.595A  pdb=" N   PHE A 296 " --> pdb=" O   ASN A 293 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 297 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 293 through 297'
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 4.229A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN A 329 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 388 through 397
      removed outlier: 3.605A  pdb=" N   HIS A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LYS A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 397 " --> pdb=" O   HIS A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 3.900A  pdb=" N   TRP A 407 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 3.658A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG A 422 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP A 424 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   MET A 425 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   LEU A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   TYR A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 29
      removed outlier: 3.771A  pdb=" N   ALA B  18 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER B  25 " --> pdb=" O   TRP B  21 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASP B  26 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLU B  27 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   HIS B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 47
      removed outlier: 4.423A  pdb=" N   LEU B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 51
      removed outlier: 3.551A  pdb=" N   VAL B  51 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 48 through 51'
    Processing helix  chain 'B' and resid 71 through 81
      removed outlier: 4.405A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 114 through 126
      removed outlier: 4.309A  pdb=" N   VAL B 121 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 148
      removed outlier: 3.967A  pdb=" N   SER B 147 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 161
      removed outlier: 4.050A  pdb=" N   GLU B 159 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU B 160 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 196
      removed outlier: 4.107A  pdb=" N   THR B 188 " --> pdb=" O   PRO B 184 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LEU B 189 " --> pdb=" O   TYR B 185 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   SER B 190 " --> pdb=" O   ASN B 186 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   HIS B 192 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   GLN B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU B 194 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL B 195 " --> pdb=" O   VAL B 191 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   GLU B 196 " --> pdb=" O   HIS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 215
      removed outlier: 3.887A  pdb=" N   ASP B 211 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   CYS B 213 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 4.111A  pdb=" N   HIS B 229 " --> pdb=" O   GLY B 225 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ALA B 233 " --> pdb=" O   HIS B 229 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY B 237 " --> pdb=" O   ALA B 233 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 259
      removed outlier: 3.797A  pdb=" N   ASN B 258 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 296
      removed outlier: 3.779A  pdb=" N   GLN B 293 " --> pdb=" O   PRO B 289 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLN B 294 " --> pdb=" O   GLU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.776A  pdb=" N   GLN B 336 " --> pdb=" O   MET B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
      removed outlier: 3.776A  pdb=" N   PHE B 343 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 340 through 343'
    Processing helix  chain 'B' and resid 384 through 401
      removed outlier: 3.619A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS B 389 " --> pdb=" O   GLN B 385 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   GLN B 394 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B 397 " --> pdb=" O   GLU B 393 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   MET B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.795A  pdb=" N   GLY B 410 " --> pdb=" O   HIS B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 433
      removed outlier: 3.514A  pdb=" N   GLU B 420 " --> pdb=" O   MET B 416 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLU B 422 " --> pdb=" O   PHE B 418 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER B 423 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL B 429 " --> pdb=" O   MET B 425 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR B 432 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68
      removed outlier: 9.087A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A 168 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68
      removed outlier: 9.087A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 270
    Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 354
    Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68
      removed outlier: 8.693A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   VAL B  68 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   PHE B 135 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE B 165 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE B 135 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   HIS B 139 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B 171 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TYR B 202 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56
    Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 356
      removed outlier: 3.748A  pdb=" N   THR B 314 " --> pdb=" O   ASN B 380 " (cutoff:3.500A)

    176 hydrogen bonds defined for protein.
    495 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1172
        1.32 -     1.44: 1885
        1.44 -     1.56: 3844
        1.56 -     1.69: 15
        1.69 -     1.81: 74
  Bond restraints: 6990
  Sorted by residual:
  bond pdb=" O3B G2P B 501 "
       pdb=" PG  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.716  1.585  0.131 2.00e-02 2.50e+03 4.28e+01
  bond pdb=" O5' G2P B 501 "
       pdb=" PA  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.656  1.574  0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" C5  GTP A 501 "
       pdb=" C6  GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.390  1.463 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C01 TA1 B 503 "
       pdb=" C45 TA1 B 503 "
    ideal  model  delta    sigma   weight residual
    1.553  1.615 -0.062 2.00e-02 2.50e+03 9.71e+00
  bond pdb=" C3A G2P B 501 "
       pdb=" PB  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.850  1.796  0.054 2.00e-02 2.50e+03 7.35e+00
  ... (remaining 6985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 9353
        3.46 -     6.92: 129
        6.92 -    10.38: 20
       10.38 -    13.84: 8
       13.84 -    17.30: 2
  Bond angle restraints: 9512
  Sorted by residual:
  angle pdb=" C14 TA1 B 503 "
        pdb=" C11 TA1 B 503 "
        pdb=" O04 TA1 B 503 "
      ideal   model   delta    sigma   weight residual
     119.42  102.12   17.30 3.00e+00 1.11e-01 3.33e+01
  angle pdb=" C10 TA1 B 503 "
        pdb=" C18 TA1 B 503 "
        pdb=" C20 TA1 B 503 "
      ideal   model   delta    sigma   weight residual
     104.78  120.74  -15.96 3.00e+00 1.11e-01 2.83e+01
  angle pdb=" O2A G2P B 501 "
        pdb=" PA  G2P B 501 "
        pdb=" O5' G2P B 501 "
      ideal   model   delta    sigma   weight residual
     107.71  121.30  -13.59 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C3' G2P B 501 "
        pdb=" C2' G2P B 501 "
        pdb=" O2' G2P B 501 "
      ideal   model   delta    sigma   weight residual
     116.29  103.49   12.80 3.00e+00 1.11e-01 1.82e+01
  angle pdb=" O1A G2P B 501 "
        pdb=" PA  G2P B 501 "
        pdb=" O2A G2P B 501 "
      ideal   model   delta    sigma   weight residual
     117.48  105.46   12.02 3.00e+00 1.11e-01 1.60e+01
  ... (remaining 9507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.48: 4147
       33.48 -    66.97: 57
       66.97 -   100.45: 12
      100.45 -   133.93: 13
      133.93 -   167.41: 7
  Dihedral angle restraints: 4236
    sinusoidal: 1765
      harmonic: 2471
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -123.32 -167.41     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -53.53  158.12     1      2.00e+01 2.50e-03 4.63e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  131.59  142.53     1      2.00e+01 2.50e-03 4.30e+01
  ... (remaining 4233 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 790
       0.072 -    0.145: 226
       0.145 -    0.217: 21
       0.217 -    0.289: 2
       0.289 -    0.361: 3
  Chirality restraints: 1042
  Sorted by residual:
  chirality pdb=" C10 TA1 B 503 "
            pdb=" C02 TA1 B 503 "
            pdb=" C11 TA1 B 503 "
            pdb=" C18 TA1 B 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.18    0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" C26 TA1 B 503 "
            pdb=" C25 TA1 B 503 "
            pdb=" C43 TA1 B 503 "
            pdb=" O11 TA1 B 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" CB  VAL A 182 "
            pdb=" CA  VAL A 182 "
            pdb=" CG1 VAL A 182 "
            pdb=" CG2 VAL A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.21e+00
  ... (remaining 1039 not shown)

  Planarity restraints: 1231
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C03 TA1 B 503 "    0.004 2.00e-02 2.50e+03   3.19e-02 1.79e+01
        pdb=" C04 TA1 B 503 "    0.046 2.00e-02 2.50e+03
        pdb=" C05 TA1 B 503 "   -0.057 2.00e-02 2.50e+03
        pdb=" C06 TA1 B 503 "    0.021 2.00e-02 2.50e+03
        pdb=" C07 TA1 B 503 "    0.023 2.00e-02 2.50e+03
        pdb=" C08 TA1 B 503 "   -0.026 2.00e-02 2.50e+03
        pdb=" C09 TA1 B 503 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C03 TA1 B 503 "    0.053 2.00e-02 2.50e+03   3.07e-02 9.44e+00
        pdb=" C04 TA1 B 503 "   -0.015 2.00e-02 2.50e+03
        pdb=" O02 TA1 B 503 "   -0.017 2.00e-02 2.50e+03
        pdb=" O03 TA1 B 503 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  31 "   -0.046 5.00e-02 4.00e+02   6.92e-02 7.66e+00
        pdb=" N   PRO B  32 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1228 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 96
        2.59 -     3.17: 5570
        3.17 -     3.75: 10399
        3.75 -     4.32: 14846
        4.32 -     4.90: 23677
  Nonbonded interactions: 54588
  Sorted by model distance:
  nonbonded pdb=" O2G G2P B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     2.019 2.170
  nonbonded pdb=" O1B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.064 2.170
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.107 2.170
  nonbonded pdb=" OD1 ASN B 101 "
            pdb=" O3G G2P B 501 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE2 GLU B  27 "
            pdb=" OG  SER B 236 "
     model   vdw
     2.275 3.040
  ... (remaining 54583 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:             0.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     8.490
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
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      :  0.009   0.131   6990  Z= 0.402
  Angle     :  1.175  17.302   9512  Z= 0.583
  Chirality :  0.065   0.361   1042
  Planarity :  0.008   0.069   1231
  Dihedral  : 16.637 167.414   2652
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.21 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -5.22 (0.21), residues: 850
  helix: -4.20 (0.14), residues: 330
  sheet: -3.16 (0.39), residues: 132
  loop : -2.73 (0.26), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  64 
 TYR   0.036   0.004   TYR B 312 
 PHE   0.028   0.004   PHE A 351 
 TRP   0.026   0.004   TRP A 346 
 HIS   0.014   0.003   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00899 ( 6990)
  covalent geometry    : angle       1.17452 ( 9512)
  hydrogen bonds       : bond        0.30038 (  176)
  hydrogen bonds       : angle      10.20210 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 219
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7601 (tt0)
REVERT: A  176 GLN cc_start: 0.8098 (mm110) cc_final: 0.7790 (mm110)
REVERT: A  302 MET cc_start: 0.8358 (mmp) cc_final: 0.7880 (mmm)
REVERT: A  313 MET cc_start: 0.7282 (mtt) cc_final: 0.7031 (mtp)
REVERT: A  388 TRP cc_start: 0.5549 (m-10) cc_final: 0.5184 (m-10)
REVERT: A  397 LEU cc_start: 0.8594 (mt) cc_final: 0.8384 (mt)
REVERT: B    1 MET cc_start: 0.6986 (mmt) cc_final: 0.6196 (tmm)
REVERT: B    6 HIS cc_start: 0.7620 (t70) cc_final: 0.7091 (t-170)
REVERT: B   37 HIS cc_start: 0.7721 (m90) cc_final: 0.7375 (m170)
REVERT: B  110 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7779 (tt0)
REVERT: B  247 GLN cc_start: 0.8092 (mt0) cc_final: 0.7853 (tt0)
REVERT: B  282 GLN cc_start: 0.8400 (mm110) cc_final: 0.7598 (mp10)
REVERT: B  300 ASN cc_start: 0.8709 (t160) cc_final: 0.8207 (m-40)
REVERT: B  325 MET cc_start: 0.8389 (mmm) cc_final: 0.8093 (tpt)
REVERT: B  330 GLU cc_start: 0.8808 (tt0) cc_final: 0.8487 (tp30)
REVERT: B  333 LEU cc_start: 0.9134 (tp) cc_final: 0.8767 (tp)
REVERT: B  417 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7580 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 220
  average time/residue: 0.0934
  time to fit residues: 26.6083
Evaluate side-chains
  145 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A  88 HIS
A 256 GLN
A 258 ASN
A 372 GLN
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
B 192 HIS
B 249 ASN
B 258 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
B 406 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.127487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.106374 restraints weight = 12183.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.110294 restraints weight = 6410.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.113051 restraints weight = 4159.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.114869 restraints weight = 3044.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.116297 restraints weight = 2437.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6990  Z= 0.186
  Angle     :  0.713   9.168   9512  Z= 0.355
  Chirality :  0.049   0.466   1042
  Planarity :  0.006   0.063   1231
  Dihedral  : 14.262 176.706   1084
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 10.62 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -4.02 (0.25), residues: 850
  helix: -2.98 (0.21), residues: 358
  sheet: -2.61 (0.41), residues: 139
  loop : -2.08 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 158 
 TYR   0.022   0.002   TYR B 312 
 PHE   0.022   0.002   PHE A 395 
 TRP   0.013   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 6990)
  covalent geometry    : angle       0.71260 ( 9512)
  hydrogen bonds       : bond        0.04909 (  176)
  hydrogen bonds       : angle       6.02263 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6949 (mt)
REVERT: A  176 GLN cc_start: 0.8218 (mm110) cc_final: 0.7894 (mm110)
REVERT: A  280 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7479 (mtpp)
REVERT: A  313 MET cc_start: 0.7368 (mtt) cc_final: 0.7122 (mtp)
REVERT: A  378 LEU cc_start: 0.9042 (mp) cc_final: 0.8823 (mp)
REVERT: A  413 MET cc_start: 0.6486 (tpt) cc_final: 0.5870 (mtp)
REVERT: B   26 ASP cc_start: 0.8107 (m-30) cc_final: 0.7608 (m-30)
REVERT: B   48 ARG cc_start: 0.7504 (mpt180) cc_final: 0.7160 (tpp80)
REVERT: B  110 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7066 (tt0)
REVERT: B  113 GLU cc_start: 0.7599 (mp0) cc_final: 0.7233 (mp0)
REVERT: B  124 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8193 (tttt)
REVERT: B  136 GLN cc_start: 0.8063 (mt0) cc_final: 0.7678 (mt0)
REVERT: B  163 ASP cc_start: 0.7901 (p0) cc_final: 0.7577 (p0)
REVERT: B  167 ASN cc_start: 0.6987 (m-40) cc_final: 0.6453 (m110)
REVERT: B  243 ARG cc_start: 0.8986 (mtm110) cc_final: 0.7642 (mtm180)
REVERT: B  293 GLN cc_start: 0.8208 (tp40) cc_final: 0.7954 (tp40)
REVERT: B  372 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8114 (ttpp)
REVERT: B  417 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7523 (tp30)
  outliers start: 20
  outliers final: 15
  residues processed: 182
  average time/residue: 0.1001
  time to fit residues: 23.6579
Evaluate side-chains
  152 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  372 GLN
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0030
   chunk 67 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 83 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    4.5998

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 197 HIS
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 329 ASN
A 406 HIS
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.126924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.106153 restraints weight = 12147.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.110135 restraints weight = 6410.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.112935 restraints weight = 4150.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.114884 restraints weight = 3029.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.116233 restraints weight = 2397.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6990  Z= 0.149
  Angle     :  0.627   9.276   9512  Z= 0.312
  Chirality :  0.047   0.296   1042
  Planarity :  0.005   0.063   1231
  Dihedral  : 12.866 178.008   1084
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.38 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -3.51 (0.26), residues: 850
  helix: -2.43 (0.23), residues: 369
  sheet: -2.30 (0.43), residues: 134
  loop : -1.97 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 158 
 TYR   0.019   0.001   TYR B 312 
 PHE   0.022   0.002   PHE B 395 
 TRP   0.013   0.002   TRP A 388 
 HIS   0.006   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6990)
  covalent geometry    : angle       0.62722 ( 9512)
  hydrogen bonds       : bond        0.04376 (  176)
  hydrogen bonds       : angle       5.37003 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  280 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6894 (tptt)
REVERT: A  302 MET cc_start: 0.8269 (mmp) cc_final: 0.7937 (mmm)
REVERT: A  313 MET cc_start: 0.7359 (mtt) cc_final: 0.7048 (mtp)
REVERT: A  378 LEU cc_start: 0.9022 (mp) cc_final: 0.8819 (mp)
REVERT: A  413 MET cc_start: 0.6701 (tpt) cc_final: 0.6038 (mtp)
REVERT: B   26 ASP cc_start: 0.7914 (m-30) cc_final: 0.7547 (m-30)
REVERT: B  110 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7266 (tt0)
REVERT: B  124 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8237 (tttt)
REVERT: B  136 GLN cc_start: 0.7657 (mt0) cc_final: 0.7309 (mt0)
REVERT: B  163 ASP cc_start: 0.7797 (p0) cc_final: 0.7488 (p0)
REVERT: B  243 ARG cc_start: 0.8905 (mtm110) cc_final: 0.7653 (mtm180)
REVERT: B  372 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8123 (ttpp)
REVERT: B  417 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7440 (tp30)
  outliers start: 19
  outliers final: 12
  residues processed: 159
  average time/residue: 0.0859
  time to fit residues: 17.9550
Evaluate side-chains
  144 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  300 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 76 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 258 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 = 0.4000 r_free = 0.4000 target = 0.125537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.105407 restraints weight = 12246.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.109254 restraints weight = 6369.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.111944 restraints weight = 4106.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.113783 restraints weight = 2990.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.115127 restraints weight = 2368.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6990  Z= 0.158
  Angle     :  0.614   9.383   9512  Z= 0.307
  Chirality :  0.046   0.254   1042
  Planarity :  0.005   0.063   1231
  Dihedral  : 12.774 177.880   1084
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 13.66 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -3.05 (0.27), residues: 850
  helix: -2.02 (0.24), residues: 364
  sheet: -2.09 (0.42), residues: 141
  loop : -1.74 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 322 
 TYR   0.018   0.002   TYR B 312 
 PHE   0.022   0.002   PHE A 395 
 TRP   0.015   0.002   TRP A 388 
 HIS   0.011   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6990)
  covalent geometry    : angle       0.61391 ( 9512)
  hydrogen bonds       : bond        0.03982 (  176)
  hydrogen bonds       : angle       5.11039 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  280 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6796 (tptt)
REVERT: A  302 MET cc_start: 0.8319 (mmp) cc_final: 0.8047 (mmm)
REVERT: A  413 MET cc_start: 0.6695 (tpt) cc_final: 0.6037 (mtp)
REVERT: B   26 ASP cc_start: 0.7829 (m-30) cc_final: 0.7397 (m-30)
REVERT: B  110 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7356 (tt0)
REVERT: B  124 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8274 (tttt)
REVERT: B  163 ASP cc_start: 0.7734 (p0) cc_final: 0.7445 (p0)
REVERT: B  417 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7389 (tp30)
  outliers start: 29
  outliers final: 22
  residues processed: 155
  average time/residue: 0.0891
  time to fit residues: 18.5495
Evaluate side-chains
  154 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  428 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 46 optimal weight:   30.0000
   chunk 79 optimal weight:   10.0000
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  14 ASN
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.123771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.103770 restraints weight = 12450.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.107732 restraints weight = 6308.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.110471 restraints weight = 4010.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.112318 restraints weight = 2901.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.113522 restraints weight = 2290.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6990  Z= 0.208
  Angle     :  0.657   9.199   9512  Z= 0.329
  Chirality :  0.048   0.235   1042
  Planarity :  0.005   0.065   1231
  Dihedral  : 12.850 177.168   1084
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 14.21 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.88 (0.27), residues: 850
  helix: -1.89 (0.24), residues: 371
  sheet: -2.13 (0.42), residues: 140
  loop : -1.56 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 322 
 TYR   0.020   0.002   TYR B 312 
 PHE   0.022   0.002   PHE A 395 
 TRP   0.016   0.002   TRP A 388 
 HIS   0.007   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 6990)
  covalent geometry    : angle       0.65738 ( 9512)
  hydrogen bonds       : bond        0.04144 (  176)
  hydrogen bonds       : angle       5.19729 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8191 (m-80)
REVERT: A  280 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6846 (tptt)
REVERT: A  302 MET cc_start: 0.8503 (mmp) cc_final: 0.7758 (mmm)
REVERT: A  413 MET cc_start: 0.6657 (tpt) cc_final: 0.6004 (mtp)
REVERT: B   26 ASP cc_start: 0.7912 (m-30) cc_final: 0.7488 (m-30)
REVERT: B  110 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7373 (tt0)
REVERT: B  124 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8202 (tttt)
REVERT: B  163 ASP cc_start: 0.7876 (p0) cc_final: 0.7611 (p0)
REVERT: B  372 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8061 (ttpp)
REVERT: B  417 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7394 (tp30)
  outliers start: 28
  outliers final: 25
  residues processed: 146
  average time/residue: 0.0843
  time to fit residues: 16.6419
Evaluate side-chains
  146 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  300 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:   20.0000
   chunk 60 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
B 337 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.127514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.106342 restraints weight = 12072.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.110594 restraints weight = 6171.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.113432 restraints weight = 3936.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.115304 restraints weight = 2866.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.116758 restraints weight = 2283.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6990  Z= 0.152
  Angle     :  0.607   9.038   9512  Z= 0.298
  Chirality :  0.047   0.232   1042
  Planarity :  0.004   0.062   1231
  Dihedral  : 12.542 179.786   1084
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 15.45 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.53 (0.28), residues: 850
  helix: -1.52 (0.25), residues: 373
  sheet: -2.02 (0.43), residues: 140
  loop : -1.44 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 322 
 TYR   0.016   0.001   TYR B  52 
 PHE   0.025   0.002   PHE A 395 
 TRP   0.016   0.002   TRP A 388 
 HIS   0.007   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6990)
  covalent geometry    : angle       0.60660 ( 9512)
  hydrogen bonds       : bond        0.03631 (  176)
  hydrogen bonds       : angle       4.92579 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7781 (pt0)
REVERT: A  154 MET cc_start: 0.7268 (mmt) cc_final: 0.6374 (tpp)
REVERT: A  210 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8322 (m-80)
REVERT: A  280 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6828 (tptt)
REVERT: A  413 MET cc_start: 0.6788 (tpt) cc_final: 0.6279 (mtp)
REVERT: B   26 ASP cc_start: 0.7885 (m-30) cc_final: 0.7467 (m-30)
REVERT: B  110 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7371 (tt0)
REVERT: B  124 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8166 (tttt)
REVERT: B  163 ASP cc_start: 0.7829 (p0) cc_final: 0.7514 (p0)
REVERT: B  230 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8002 (mt)
REVERT: B  372 LYS cc_start: 0.8520 (ttpp) cc_final: 0.7995 (ttpp)
REVERT: B  391 ILE cc_start: 0.7625 (mm) cc_final: 0.7287 (mt)
REVERT: B  395 PHE cc_start: 0.7283 (t80) cc_final: 0.6889 (t80)
REVERT: B  417 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7483 (tp30)
  outliers start: 32
  outliers final: 27
  residues processed: 150
  average time/residue: 0.0813
  time to fit residues: 16.5917
Evaluate side-chains
  152 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  428 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 66 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 76 optimal weight:   30.0000
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  28 HIS
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
B 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.124448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.103381 restraints weight = 12181.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.107403 restraints weight = 6328.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.110161 restraints weight = 4096.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.112039 restraints weight = 3013.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.113294 restraints weight = 2399.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6990  Z= 0.221
  Angle     :  0.660   8.881   9512  Z= 0.331
  Chirality :  0.049   0.248   1042
  Planarity :  0.005   0.066   1231
  Dihedral  : 12.516 177.995   1084
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 16.14 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.62 (0.28), residues: 850
  helix: -1.50 (0.25), residues: 371
  sheet: -2.26 (0.41), residues: 143
  loop : -1.51 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 322 
 TYR   0.019   0.002   TYR B 312 
 PHE   0.024   0.002   PHE A 395 
 TRP   0.016   0.002   TRP A 388 
 HIS   0.005   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 6990)
  covalent geometry    : angle       0.66026 ( 9512)
  hydrogen bonds       : bond        0.04127 (  176)
  hydrogen bonds       : angle       5.24316 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8030 (pt0)
REVERT: A  210 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8358 (m-80)
REVERT: A  280 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6908 (tptt)
REVERT: A  413 MET cc_start: 0.6667 (tpt) cc_final: 0.6184 (mtp)
REVERT: B   26 ASP cc_start: 0.7927 (m-30) cc_final: 0.7524 (m-30)
REVERT: B  110 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7399 (tt0)
REVERT: B  124 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8178 (tttt)
REVERT: B  163 ASP cc_start: 0.7875 (p0) cc_final: 0.7654 (p0)
REVERT: B  391 ILE cc_start: 0.7650 (mm) cc_final: 0.7316 (mt)
  outliers start: 31
  outliers final: 28
  residues processed: 144
  average time/residue: 0.0835
  time to fit residues: 16.3290
Evaluate side-chains
  146 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  428 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 79 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 69 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0970
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    5.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.126503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.105354 restraints weight = 12033.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.109496 restraints weight = 6145.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.112272 restraints weight = 3934.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.114250 restraints weight = 2886.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.115439 restraints weight = 2281.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6990  Z= 0.160
  Angle     :  0.612   8.859   9512  Z= 0.304
  Chirality :  0.047   0.238   1042
  Planarity :  0.005   0.066   1231
  Dihedral  : 12.195 179.945   1084
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 15.86 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -2.16 (0.28), residues: 850
  helix: -1.11 (0.27), residues: 366
  sheet: -2.01 (0.42), residues: 140
  loop : -1.31 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 322 
 TYR   0.013   0.001   TYR B 312 
 PHE   0.023   0.002   PHE A 395 
 TRP   0.015   0.002   TRP A 388 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6990)
  covalent geometry    : angle       0.61190 ( 9512)
  hydrogen bonds       : bond        0.03640 (  176)
  hydrogen bonds       : angle       5.01945 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7956 (pt0)
REVERT: A  210 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8362 (m-80)
REVERT: A  413 MET cc_start: 0.6957 (tpt) cc_final: 0.6206 (mtt)
REVERT: B   26 ASP cc_start: 0.8003 (m-30) cc_final: 0.7600 (m-30)
REVERT: B  110 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7313 (tt0)
REVERT: B  124 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8170 (tttt)
REVERT: B  163 ASP cc_start: 0.7759 (p0) cc_final: 0.7463 (p0)
REVERT: B  372 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8039 (ttpp)
REVERT: B  390 ARG cc_start: 0.8270 (mtm110) cc_final: 0.7930 (ptm160)
REVERT: B  391 ILE cc_start: 0.7572 (mm) cc_final: 0.7230 (mt)
  outliers start: 38
  outliers final: 30
  residues processed: 145
  average time/residue: 0.0832
  time to fit residues: 16.4064
Evaluate side-chains
  148 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  428 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 42 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 54 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    3.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.128765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.107720 restraints weight = 11935.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.111950 restraints weight = 6086.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.114851 restraints weight = 3882.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.116832 restraints weight = 2808.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.118166 restraints weight = 2210.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6990  Z= 0.120
  Angle     :  0.584   8.792   9512  Z= 0.286
  Chirality :  0.045   0.205   1042
  Planarity :  0.004   0.066   1231
  Dihedral  : 11.811 178.246   1084
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.55 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -1.75 (0.29), residues: 850
  helix: -0.80 (0.28), residues: 363
  sheet: -1.76 (0.43), residues: 140
  loop : -1.08 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 322 
 TYR   0.012   0.001   TYR B 312 
 PHE   0.042   0.002   PHE B 268 
 TRP   0.015   0.001   TRP A  21 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6990)
  covalent geometry    : angle       0.58426 ( 9512)
  hydrogen bonds       : bond        0.03309 (  176)
  hydrogen bonds       : angle       4.77899 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7924 (pt0)
REVERT: A  154 MET cc_start: 0.7134 (mmt) cc_final: 0.6213 (tpp)
REVERT: A  210 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8236 (m-80)
REVERT: A  271 THR cc_start: 0.8144 (t) cc_final: 0.7565 (m)
REVERT: A  413 MET cc_start: 0.6891 (tpt) cc_final: 0.6153 (mtt)
REVERT: B   19 LYS cc_start: 0.8211 (tptt) cc_final: 0.7890 (tppt)
REVERT: B   26 ASP cc_start: 0.7913 (m-30) cc_final: 0.7519 (m-30)
REVERT: B  110 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7360 (tt0)
REVERT: B  124 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8120 (tttt)
REVERT: B  163 ASP cc_start: 0.7663 (p0) cc_final: 0.7326 (p0)
REVERT: B  243 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8182 (mtm180)
REVERT: B  269 MET cc_start: 0.8004 (ptp) cc_final: 0.7641 (ptp)
REVERT: B  372 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8000 (ttpp)
REVERT: B  390 ARG cc_start: 0.8308 (mtm110) cc_final: 0.8019 (ptm160)
REVERT: B  391 ILE cc_start: 0.7524 (mm) cc_final: 0.7185 (mt)
  outliers start: 29
  outliers final: 26
  residues processed: 146
  average time/residue: 0.0889
  time to fit residues: 17.3723
Evaluate side-chains
  150 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  428 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 67 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0030
   chunk 3 optimal weight:   30.0000
   overall best weight:    4.9998

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.127441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.106210 restraints weight = 11919.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.110386 restraints weight = 6126.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.113202 restraints weight = 3929.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.115051 restraints weight = 2876.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.116496 restraints weight = 2307.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6990  Z= 0.152
  Angle     :  0.620   8.558   9512  Z= 0.304
  Chirality :  0.046   0.220   1042
  Planarity :  0.005   0.066   1231
  Dihedral  : 11.880 179.082   1084
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.69 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -1.72 (0.29), residues: 850
  helix: -0.79 (0.28), residues: 365
  sheet: -1.72 (0.43), residues: 140
  loop : -1.05 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 123 
 TYR   0.020   0.002   TYR A 172 
 PHE   0.036   0.002   PHE B 268 
 TRP   0.014   0.002   TRP A 388 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6990)
  covalent geometry    : angle       0.61961 ( 9512)
  hydrogen bonds       : bond        0.03571 (  176)
  hydrogen bonds       : angle       4.84206 (  495)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7885 (pt0)
REVERT: A  210 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8290 (m-80)
REVERT: A  413 MET cc_start: 0.6875 (tpt) cc_final: 0.6088 (mtp)
REVERT: B   19 LYS cc_start: 0.8259 (tptt) cc_final: 0.7925 (tppt)
REVERT: B   26 ASP cc_start: 0.7959 (m-30) cc_final: 0.7484 (m-30)
REVERT: B  110 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7462 (tt0)
REVERT: B  124 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8159 (tttt)
REVERT: B  163 ASP cc_start: 0.7810 (p0) cc_final: 0.7481 (p0)
REVERT: B  372 LYS cc_start: 0.8534 (ttpp) cc_final: 0.7981 (ttpp)
REVERT: B  390 ARG cc_start: 0.8331 (mtm110) cc_final: 0.7960 (ptm160)
REVERT: B  391 ILE cc_start: 0.7514 (mm) cc_final: 0.7144 (mt)
REVERT: B  395 PHE cc_start: 0.7243 (t80) cc_final: 0.6814 (t80)
  outliers start: 29
  outliers final: 26
  residues processed: 137
  average time/residue: 0.0862
  time to fit residues: 16.0504
Evaluate side-chains
  149 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   85 GLN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  428 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 68 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   chunk 29 optimal weight:    0.1980
   chunk 35 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    6.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.126338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.105019 restraints weight = 11999.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.109113 restraints weight = 6190.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.111915 restraints weight = 4009.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.113763 restraints weight = 2946.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.115176 restraints weight = 2367.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6990  Z= 0.174
  Angle     :  0.640   8.234   9512  Z= 0.315
  Chirality :  0.047   0.227   1042
  Planarity :  0.005   0.066   1231
  Dihedral  : 11.976 179.815   1084
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.83 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -1.81 (0.29), residues: 850
  helix: -0.88 (0.27), residues: 366
  sheet: -1.77 (0.43), residues: 140
  loop : -1.07 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 123 
 TYR   0.020   0.002   TYR A 172 
 PHE   0.035   0.002   PHE B 268 
 TRP   0.014   0.002   TRP A 388 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6990)
  covalent geometry    : angle       0.63964 ( 9512)
  hydrogen bonds       : bond        0.03758 (  176)
  hydrogen bonds       : angle       4.96006 (  495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1240.87 seconds
wall clock time: 22 minutes 9.78 seconds (1329.78 seconds total)