Starting phenix.real_space_refine
on Wed Sep 17 14:34:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xsr_38626/09_2025/8xsr_38626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xsr_38626/09_2025/8xsr_38626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xsr_38626/09_2025/8xsr_38626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xsr_38626/09_2025/8xsr_38626.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xsr_38626/09_2025/8xsr_38626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xsr_38626/09_2025/8xsr_38626.map"
  }
  resolution = 2.93
  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=   0.001 sd=   0.101
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       5      5.49       5
     Mg      2      5.21       5
     S      33      5.16       5
     C    5777      2.51       5
     N    1613      2.21       5
     O    1700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 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: 9130
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4348
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 19, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 4722
          Classifications: {'peptide': 616}
          Link IDs: {'PTRANS': 18, 'TRANS': 597}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.48, per 1000 atoms: 0.27
  Number of scatterers: 9130
  At special positions: 0
  Unit cell: (69.056, 94.848, 148.928, 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      33     16.00
     P       5     15.00
     Mg      2     11.99
     O    1700      8.00
     N    1613      7.00
     C    5777      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: 0.91
  Conformation dependent library (CDL) restraints added in 340.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2190

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      61.5% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid -1 through 10
      removed outlier: 3.677A  pdb=" N   GLN A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 30
      removed outlier: 3.693A  pdb=" N   VAL A  19 " --> pdb=" O   TRP A  15 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   VAL A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE A  26 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 45
    Processing helix  chain 'A' and resid 51 through 71
      removed outlier: 3.928A  pdb=" N   VAL A  55 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   VAL A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 99
      removed outlier: 3.596A  pdb=" N   VAL A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE A  78 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLY A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LEU A  90 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
      removed outlier: 3.902A  pdb=" N   PHE A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 135
      removed outlier: 3.562A  pdb=" N   LEU A 128 " --> pdb=" O   HIS A 124 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 153
      removed outlier: 3.548A  pdb=" N   ILE A 144 " --> pdb=" O   PRO A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 165
      removed outlier: 3.515A  pdb=" N   VAL A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 203
      removed outlier: 3.719A  pdb=" N   ILE A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      Proline residue:  A 181  - end of helix
      removed outlier: 3.735A  pdb=" N   MET A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER A 188 " --> pdb=" O   THR A 184 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLY A 192 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 220 through 238
      removed outlier: 3.620A  pdb=" N   GLU A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   TRP A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 266
      removed outlier: 3.506A  pdb=" N   ILE A 257 " --> pdb=" O   SER A 253 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TRP A 258 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 293
      removed outlier: 4.298A  pdb=" N   ILE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A 279 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 313
      removed outlier: 3.920A  pdb=" N   ARG A 300 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   CYS A 304 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 382
    Processing helix  chain 'A' and resid 400 through 402
      No H-bonds generated for 'chain 'A' and resid 400 through 402'
    Processing helix  chain 'A' and resid 403 through 410
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 437 through 448
      removed outlier: 3.890A  pdb=" N   GLU A 443 " --> pdb=" O   ASP A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 456
      removed outlier: 3.651A  pdb=" N   VAL A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 484
      removed outlier: 3.584A  pdb=" N   ARG A 479 " --> pdb=" O   GLY A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 518
      removed outlier: 3.586A  pdb=" N   VAL A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 560
      removed outlier: 3.961A  pdb=" N   ALA A 558 " --> pdb=" O   ASP A 554 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP A 559 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 31 through 50
      removed outlier: 3.620A  pdb=" N   THR B  35 " --> pdb=" O   GLN B  31 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE B  39 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU B  41 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE B  48 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 68
      removed outlier: 4.101A  pdb=" N   ARG B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE B  64 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 88
    Processing helix  chain 'B' and resid 90 through 99
      removed outlier: 3.621A  pdb=" N   ASP B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 158
      removed outlier: 3.547A  pdb=" N   VAL B 113 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA B 128 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TRP B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA B 148 " --> pdb=" O   ARG B 144 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA B 151 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLN B 154 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLU B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS B 158 " --> pdb=" O   GLN B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 166
      removed outlier: 4.043A  pdb=" N   PHE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 177
      removed outlier: 3.515A  pdb=" N   ARG B 176 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 189
      removed outlier: 3.606A  pdb=" N   GLN B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 208
      removed outlier: 3.678A  pdb=" N   LEU B 200 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL B 205 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 223
    Processing helix  chain 'B' and resid 224 through 234
      removed outlier: 3.956A  pdb=" N   THR B 231 " --> pdb=" O   SER B 227 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG B 232 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 243
      removed outlier: 3.544A  pdb=" N   VAL B 243 " --> pdb=" O   GLN B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 262
      removed outlier: 3.682A  pdb=" N   ARG B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU B 252 " --> pdb=" O   ASN B 248 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 268
    Processing helix  chain 'B' and resid 269 through 271
      No H-bonds generated for 'chain 'B' and resid 269 through 271'
    Processing helix  chain 'B' and resid 272 through 284
      removed outlier: 3.517A  pdb=" N   LYS B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 297
      removed outlier: 3.648A  pdb=" N   ALA B 293 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE B 296 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 305
    Processing helix  chain 'B' and resid 305 through 324
      removed outlier: 3.526A  pdb=" N   TYR B 312 " --> pdb=" O   GLY B 308 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA B 324 " --> pdb=" O   GLY B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 344
      removed outlier: 3.503A  pdb=" N   ALA B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN B 344 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 359
      removed outlier: 4.567A  pdb=" N   LEU B 357 " --> pdb=" O   MET B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 364
      removed outlier: 4.685A  pdb=" N   SER B 363 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA B 364 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 360 through 364'
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 429 through 438
      removed outlier: 3.534A  pdb=" N   VAL B 434 " --> pdb=" O   LYS B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.649A  pdb=" N   ALA B 465 " --> pdb=" O   GLU B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 487
    Processing helix  chain 'B' and resid 493 through 504
      removed outlier: 3.511A  pdb=" N   ALA B 500 " --> pdb=" O   GLU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 511
      removed outlier: 4.034A  pdb=" N   HIS B 511 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 543
    Processing helix  chain 'B' and resid 559 through 570
      removed outlier: 3.513A  pdb=" N   LEU B 564 " --> pdb=" O   THR B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 614
    Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341
      removed outlier: 5.308A  pdb=" N   ALA A 339 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP A 353 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414
      removed outlier: 6.605A  pdb=" N   GLY A 412 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   ASP A 496 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL A 414 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   THR A 364 " --> pdb=" O   ILE A 525 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   SER A 527 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   VAL A 366 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR A 363 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   VAL A 540 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ALA A 365 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   ILE A 542 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY A 549 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ASP A 543 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   VAL A 547 " --> pdb=" O   ASP A 543 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 394
      removed outlier: 3.578A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 424
    Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 394
    Processing sheet with id=AA6, first strand: chain 'B' and resid 467 through 470
      removed outlier: 6.416A  pdb=" N   GLY B 468 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ASP B 552 " --> pdb=" O   GLY B 468 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL B 470 " --> pdb=" O   ASP B 552 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL B 420 " --> pdb=" O   ILE B 581 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   LEU B 596 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ALA B 421 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   MET B 598 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL B 423 " --> pdb=" O   MET B 598 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU B 605 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASP B 599 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   ILE B 603 " --> pdb=" O   ASP B 599 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1293 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: 1.50

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1500
        1.31 -     1.43: 2407
        1.43 -     1.56: 5309
        1.56 -     1.68: 9
        1.68 -     1.80: 61
  Bond restraints: 9286
  Sorted by residual:
  bond pdb=" C4  ATP A 601 "
       pdb=" C5  ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.470 -0.082 1.00e-02 1.00e+04 6.74e+01
  bond pdb=" C5  ATP A 601 "
       pdb=" C6  ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.70e+01
  bond pdb=" CA  ASP B 593 "
       pdb=" C   ASP B 593 "
    ideal  model  delta    sigma   weight residual
    1.523  1.459  0.065 1.34e-02 5.57e+03 2.32e+01
  bond pdb=" C8  ATP A 601 "
       pdb=" N7  ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.310  1.356 -0.046 1.00e-02 1.00e+04 2.09e+01
  bond pdb=" C4  ATP A 601 "
       pdb=" N9  ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.374  1.329  0.045 1.00e-02 1.00e+04 2.06e+01
  ... (remaining 9281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 12488
        3.47 -     6.93: 146
        6.93 -    10.40: 14
       10.40 -    13.87: 4
       13.87 -    17.33: 1
  Bond angle restraints: 12653
  Sorted by residual:
  angle pdb=" PB  ATP A 601 "
        pdb=" O3B ATP A 601 "
        pdb=" PG  ATP A 601 "
      ideal   model   delta    sigma   weight residual
     139.87  122.54   17.33 1.00e+00 1.00e+00 3.00e+02
  angle pdb=" PA  ATP A 601 "
        pdb=" O3A ATP A 601 "
        pdb=" PB  ATP A 601 "
      ideal   model   delta    sigma   weight residual
     136.83  123.90   12.93 1.00e+00 1.00e+00 1.67e+02
  angle pdb=" N   VAL A 218 "
        pdb=" CA  VAL A 218 "
        pdb=" C   VAL A 218 "
      ideal   model   delta    sigma   weight residual
     113.71  104.05    9.66 9.50e-01 1.11e+00 1.03e+02
  angle pdb=" N   ARG A 430 "
        pdb=" CA  ARG A 430 "
        pdb=" C   ARG A 430 "
      ideal   model   delta    sigma   weight residual
     111.71   99.89   11.82 1.34e+00 5.57e-01 7.78e+01
  angle pdb=" C5  ATP A 601 "
        pdb=" C4  ATP A 601 "
        pdb=" N3  ATP A 601 "
      ideal   model   delta    sigma   weight residual
     126.80  119.05    7.75 1.00e+00 1.00e+00 6.00e+01
  ... (remaining 12648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.50: 5481
       35.50 -    71.00: 44
       71.00 -   106.50: 6
      106.50 -   142.00: 0
      142.00 -   177.50: 1
  Dihedral angle restraints: 5532
    sinusoidal: 2130
      harmonic: 3402
  Sorted by residual:
  dihedral pdb=" O2A ADP B 701 "
           pdb=" O3A ADP B 701 "
           pdb=" PA  ADP B 701 "
           pdb=" PB  ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  122.50  177.50     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" CA  LEU B 195 "
           pdb=" C   LEU B 195 "
           pdb=" N   LEU B 196 "
           pdb=" CA  LEU B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.34   29.66     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  GLU B 376 "
           pdb=" C   GLU B 376 "
           pdb=" N   SER B 377 "
           pdb=" CA  SER B 377 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.04  -25.96     0      5.00e+00 4.00e-02 2.70e+01
  ... (remaining 5529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1294
       0.071 -    0.141: 213
       0.141 -    0.212: 10
       0.212 -    0.283: 2
       0.283 -    0.353: 2
  Chirality restraints: 1521
  Sorted by residual:
  chirality pdb=" CA  ALA B 414 "
            pdb=" N   ALA B 414 "
            pdb=" C   ALA B 414 "
            pdb=" CB  ALA B 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.13    0.35 2.00e-01 2.50e+01 3.12e+00
  chirality pdb=" CA  ASP B 593 "
            pdb=" N   ASP B 593 "
            pdb=" C   ASP B 593 "
            pdb=" CB  ASP B 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.93e+00
  chirality pdb=" CB  ILE B 448 "
            pdb=" CA  ILE B 448 "
            pdb=" CG1 ILE B 448 "
            pdb=" CG2 ILE B 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1518 not shown)

  Planarity restraints: 1615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  87 "    0.012 2.00e-02 2.50e+03   2.49e-02 6.20e+00
        pdb=" C   GLY A  87 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLY A  87 "    0.016 2.00e-02 2.50e+03
        pdb=" N   HIS A  88 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 345 "    0.038 5.00e-02 4.00e+02   5.79e-02 5.36e+00
        pdb=" N   PRO B 346 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 346 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 346 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 568 "   -0.011 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   HIS B 568 "    0.040 2.00e-02 2.50e+03
        pdb=" O   HIS B 568 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ALA B 569 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1612 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 68
        2.56 -     3.14: 7553
        3.14 -     3.73: 13923
        3.73 -     4.31: 20853
        4.31 -     4.90: 33796
  Nonbonded interactions: 76193
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 375 "
            pdb="MG    MG A 602 "
     model   vdw
     1.972 2.170
  nonbonded pdb=" OG1 THR B 431 "
            pdb="MG    MG B 702 "
     model   vdw
     2.079 2.170
  nonbonded pdb=" O1B ADP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" O1B ATP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.125 2.170
  nonbonded pdb=" NH2 ARG A 185 "
            pdb=" OE2 GLU A 233 "
     model   vdw
     2.208 3.120
  ... (remaining 76188 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.320
  Find NCS groups from input model:        0.060
  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:6.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
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      :  0.006   0.082   9286  Z= 0.317
  Angle     :  1.033  17.332  12653  Z= 0.677
  Chirality :  0.052   0.353   1521
  Planarity :  0.005   0.058   1615
  Dihedral  : 10.788 177.500   3342
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.67 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  2.09 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.75 (0.17), residues: 1186
  helix: -3.78 (0.12), residues: 751
  sheet: -2.94 (0.60), residues: 60
  loop : -3.52 (0.25), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 251 
 TYR   0.011   0.002   TYR B 517 
 PHE   0.027   0.002   PHE B  64 
 TRP   0.017   0.002   TRP B 229 
 HIS   0.014   0.002   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 9286)
  covalent geometry    : angle       1.03282 (12653)
  hydrogen bonds       : bond        0.25490 (  438)
  hydrogen bonds       : angle       9.65155 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 251
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   81 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7299 (ttp-170)
REVERT: A  198 ARG cc_start: 0.7453 (ttp-170) cc_final: 0.7135 (ttm170)
REVERT: A  565 GLU cc_start: 0.8154 (tt0) cc_final: 0.7144 (mt-10)
REVERT: B   32 ARG cc_start: 0.6494 (pmt100) cc_final: 0.5702 (ptm-80)
REVERT: B   51 ILE cc_start: 0.8457 (tp) cc_final: 0.8157 (pt)
REVERT: B  100 MET cc_start: 0.8786 (ttm) cc_final: 0.8373 (ttm)
REVERT: B  194 GLN cc_start: 0.6745 (tt0) cc_final: 0.6518 (tm-30)
REVERT: B  236 ARG cc_start: 0.7351 (ptm-80) cc_final: 0.7072 (mtm110)
REVERT: B  288 GLN cc_start: 0.7623 (mt0) cc_final: 0.7350 (pt0)
REVERT: B  392 GLU cc_start: 0.7935 (tt0) cc_final: 0.6963 (tm-30)
REVERT: B  394 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7148 (mt-10)
REVERT: B  590 ARG cc_start: 0.7881 (ptt90) cc_final: 0.7390 (ptp-170)
  outliers start: 7
  outliers final: 1
  residues processed: 256
  average time/residue: 0.6242
  time to fit residues: 169.8838
Evaluate side-chains
  137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  506 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
A 130 GLN
A 172 ASN
A 187 GLN
A 337 HIS
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
B 186 ASN
B 338 GLN
B 349 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.138272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.110637 restraints weight = 10637.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.65
r_work: 0.2894 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9286  Z= 0.194
  Angle     :  0.756  10.614  12653  Z= 0.393
  Chirality :  0.046   0.220   1521
  Planarity :  0.006   0.055   1615
  Dihedral  :  9.839 166.114   1350
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 10.99 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -4.24 (0.20), residues: 1186
  helix: -2.52 (0.16), residues: 746
  sheet: -2.56 (0.61), residues: 61
  loop : -3.08 (0.26), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 624 
 TYR   0.017   0.002   TYR A 431 
 PHE   0.015   0.002   PHE B 509 
 TRP   0.013   0.001   TRP B 229 
 HIS   0.011   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 9286)
  covalent geometry    : angle       0.75555 (12653)
  hydrogen bonds       : bond        0.05015 (  438)
  hydrogen bonds       : angle       5.39103 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A    7 ARG cc_start: 0.8426 (ptt90) cc_final: 0.7901 (ttp80)
REVERT: A   81 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7386 (ttp-170)
REVERT: A  195 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7032 (tpt170)
REVERT: A  282 MET cc_start: 0.7879 (tpp) cc_final: 0.7562 (mmt)
REVERT: A  509 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7478 (mtp85)
REVERT: B   32 ARG cc_start: 0.6491 (pmt100) cc_final: 0.5251 (ptm-80)
REVERT: B  102 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7836 (pp)
REVERT: B  125 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: B  194 GLN cc_start: 0.7060 (tt0) cc_final: 0.6193 (tm-30)
REVERT: B  200 LEU cc_start: 0.7488 (mt) cc_final: 0.7284 (mt)
REVERT: B  232 ARG cc_start: 0.7167 (ttp80) cc_final: 0.6620 (ptt180)
REVERT: B  236 ARG cc_start: 0.7755 (ptm-80) cc_final: 0.7203 (mtm110)
REVERT: B  273 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7820 (mm-30)
REVERT: B  392 GLU cc_start: 0.8036 (tt0) cc_final: 0.6845 (tm-30)
REVERT: B  394 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7162 (mt-10)
REVERT: B  590 ARG cc_start: 0.8043 (ptt90) cc_final: 0.7485 (ptt-90)
REVERT: B  602 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7406 (ptm160)
  outliers start: 37
  outliers final: 19
  residues processed: 179
  average time/residue: 0.5510
  time to fit residues: 105.9275
Evaluate side-chains
  157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  273 GLU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0000
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
B 139 ASN
B 186 ASN
B 349 GLN
B 568 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.140921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.113111 restraints weight = 10568.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.65
r_work: 0.2930 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9286  Z= 0.140
  Angle     :  0.668  11.923  12653  Z= 0.346
  Chirality :  0.043   0.203   1521
  Planarity :  0.005   0.053   1615
  Dihedral  :  9.381 162.812   1350
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 13.61 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.24 (0.21), residues: 1186
  helix: -1.69 (0.17), residues: 757
  sheet: -1.78 (0.65), residues: 56
  loop : -2.88 (0.26), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 382 
 TYR   0.014   0.001   TYR A 431 
 PHE   0.011   0.001   PHE B 509 
 TRP   0.011   0.001   TRP A  15 
 HIS   0.003   0.001   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9286)
  covalent geometry    : angle       0.66828 (12653)
  hydrogen bonds       : bond        0.04077 (  438)
  hydrogen bonds       : angle       4.77230 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   81 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7166 (ttp-170)
REVERT: A  170 LEU cc_start: 0.7989 (tt) cc_final: 0.7615 (mt)
REVERT: A  195 ARG cc_start: 0.7674 (ttm170) cc_final: 0.6940 (tpt-90)
REVERT: A  282 MET cc_start: 0.7753 (tpp) cc_final: 0.7498 (mmt)
REVERT: A  409 SER cc_start: 0.8749 (t) cc_final: 0.8089 (p)
REVERT: A  509 ARG cc_start: 0.7707 (mtp180) cc_final: 0.7433 (mtp85)
REVERT: B   32 ARG cc_start: 0.6364 (pmt100) cc_final: 0.5119 (ptm-80)
REVERT: B  190 MET cc_start: 0.6400 (tmm) cc_final: 0.6196 (tmm)
REVERT: B  194 GLN cc_start: 0.6922 (tt0) cc_final: 0.6002 (tm-30)
REVERT: B  232 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6491 (ptt180)
REVERT: B  236 ARG cc_start: 0.7604 (ptm-80) cc_final: 0.7037 (mtm110)
REVERT: B  273 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7829 (mm-30)
REVERT: B  284 SER cc_start: 0.8295 (p) cc_final: 0.7996 (m)
REVERT: B  392 GLU cc_start: 0.7912 (tt0) cc_final: 0.6693 (tm-30)
REVERT: B  394 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7109 (mt-10)
REVERT: B  415 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7599 (mm-30)
REVERT: B  418 SER cc_start: 0.7082 (t) cc_final: 0.6804 (p)
REVERT: B  498 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7283 (mp)
REVERT: B  590 ARG cc_start: 0.8002 (ptt90) cc_final: 0.7440 (ptt-90)
REVERT: B  602 ARG cc_start: 0.7614 (ptp-170) cc_final: 0.7311 (ptm160)
  outliers start: 34
  outliers final: 15
  residues processed: 181
  average time/residue: 0.5837
  time to fit residues: 113.1049
Evaluate side-chains
  157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  273 GLU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  555 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 114 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
B 186 ASN
B 349 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.139515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.111447 restraints weight = 10841.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.69
r_work: 0.2913 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9286  Z= 0.140
  Angle     :  0.638  10.204  12653  Z= 0.330
  Chirality :  0.043   0.195   1521
  Planarity :  0.005   0.049   1615
  Dihedral  :  9.085 162.336   1350
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 13.72 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.60 (0.22), residues: 1186
  helix: -1.19 (0.18), residues: 764
  sheet: -1.80 (0.67), residues: 57
  loop : -2.60 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 382 
 TYR   0.012   0.001   TYR A 431 
 PHE   0.011   0.001   PHE B 509 
 TRP   0.009   0.001   TRP A  15 
 HIS   0.003   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9286)
  covalent geometry    : angle       0.63815 (12653)
  hydrogen bonds       : bond        0.03789 (  438)
  hydrogen bonds       : angle       4.51904 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 149
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.7387 (mptm) cc_final: 0.7129 (mmtp)
REVERT: A   81 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7276 (ttp-170)
REVERT: A  154 ASP cc_start: 0.7691 (t0) cc_final: 0.7234 (t0)
REVERT: A  170 LEU cc_start: 0.8015 (tt) cc_final: 0.7700 (mt)
REVERT: A  195 ARG cc_start: 0.7720 (ttm170) cc_final: 0.6951 (tpp-160)
REVERT: A  282 MET cc_start: 0.7851 (tpp) cc_final: 0.7598 (mmt)
REVERT: A  409 SER cc_start: 0.8782 (t) cc_final: 0.8140 (p)
REVERT: A  431 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8473 (m-80)
REVERT: A  509 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7442 (mtp85)
REVERT: B   26 ARG cc_start: 0.8225 (ptm160) cc_final: 0.7941 (ptm160)
REVERT: B   32 ARG cc_start: 0.6376 (pmt100) cc_final: 0.5111 (ptm-80)
REVERT: B  194 GLN cc_start: 0.6886 (tt0) cc_final: 0.6244 (tm-30)
REVERT: B  210 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: B  232 ARG cc_start: 0.7161 (ttp80) cc_final: 0.6647 (ptt180)
REVERT: B  236 ARG cc_start: 0.7583 (ptm-80) cc_final: 0.7060 (mtm110)
REVERT: B  272 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7175 (mtp85)
REVERT: B  273 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8023 (mp0)
REVERT: B  284 SER cc_start: 0.8346 (p) cc_final: 0.8061 (m)
REVERT: B  347 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.5599 (tp)
REVERT: B  357 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7378 (tp)
REVERT: B  392 GLU cc_start: 0.7922 (tt0) cc_final: 0.6604 (tp30)
REVERT: B  394 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7215 (mt-10)
REVERT: B  590 ARG cc_start: 0.8042 (ptt90) cc_final: 0.7480 (ptt-90)
REVERT: B  594 LEU cc_start: 0.8060 (tp) cc_final: 0.7780 (tp)
REVERT: B  602 ARG cc_start: 0.7736 (ptp-170) cc_final: 0.7343 (ptm160)
  outliers start: 50
  outliers final: 25
  residues processed: 184
  average time/residue: 0.5937
  time to fit residues: 117.0349
Evaluate side-chains
  171 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 TYR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  273 GLU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  573 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 94 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
A 320 ASN
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 ASN
B 349 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.109564 restraints weight = 10873.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.76
r_work: 0.3097 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9286  Z= 0.132
  Angle     :  0.623  11.423  12653  Z= 0.321
  Chirality :  0.043   0.185   1521
  Planarity :  0.004   0.047   1615
  Dihedral  :  8.806 160.623   1350
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 15.60 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.10 (0.23), residues: 1186
  helix: -0.80 (0.18), residues: 765
  sheet: -1.78 (0.67), residues: 57
  loop : -2.39 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 382 
 TYR   0.012   0.001   TYR A 431 
 PHE   0.011   0.001   PHE B 509 
 TRP   0.009   0.001   TRP A  15 
 HIS   0.002   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9286)
  covalent geometry    : angle       0.62348 (12653)
  hydrogen bonds       : bond        0.03615 (  438)
  hydrogen bonds       : angle       4.36825 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 146
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.7798 (mptm) cc_final: 0.7596 (mmtp)
REVERT: A   81 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7730 (ttp-170)
REVERT: A  170 LEU cc_start: 0.8278 (tt) cc_final: 0.8020 (mt)
REVERT: A  195 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7575 (tpp-160)
REVERT: A  282 MET cc_start: 0.8208 (tpp) cc_final: 0.7931 (mmt)
REVERT: A  307 ARG cc_start: 0.8705 (mtm-85) cc_final: 0.8499 (mtt180)
REVERT: A  392 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7933 (mm)
REVERT: A  409 SER cc_start: 0.9017 (t) cc_final: 0.8436 (p)
REVERT: A  487 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7772 (pp)
REVERT: A  509 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7746 (mtp85)
REVERT: B   26 ARG cc_start: 0.8465 (ptm160) cc_final: 0.8210 (ptm160)
REVERT: B   32 ARG cc_start: 0.6724 (pmt100) cc_final: 0.5516 (ptm-80)
REVERT: B  194 GLN cc_start: 0.7008 (tt0) cc_final: 0.6366 (tm-30)
REVERT: B  232 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7034 (ptt180)
REVERT: B  236 ARG cc_start: 0.7752 (ptm-80) cc_final: 0.7426 (mtm110)
REVERT: B  272 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7404 (mtp85)
REVERT: B  273 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (mp0)
REVERT: B  284 SER cc_start: 0.8460 (p) cc_final: 0.8249 (m)
REVERT: B  304 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8803 (p)
REVERT: B  347 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.5853 (tp)
REVERT: B  357 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7741 (tp)
REVERT: B  392 GLU cc_start: 0.8161 (tt0) cc_final: 0.7078 (tp30)
REVERT: B  394 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7505 (mt-10)
REVERT: B  498 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7828 (mp)
REVERT: B  578 THR cc_start: 0.8851 (t) cc_final: 0.8582 (m)
REVERT: B  590 ARG cc_start: 0.8207 (ptt90) cc_final: 0.7769 (ptt-90)
REVERT: B  602 ARG cc_start: 0.8092 (ptp-170) cc_final: 0.7795 (ptm160)
  outliers start: 43
  outliers final: 25
  residues processed: 176
  average time/residue: 0.5734
  time to fit residues: 108.1522
Evaluate side-chains
  169 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  273 GLU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  573 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 107 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
A 428 ASN
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 358 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.139820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111613 restraints weight = 10705.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.67
r_work: 0.2928 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9286  Z= 0.130
  Angle     :  0.622  12.966  12653  Z= 0.316
  Chirality :  0.042   0.176   1521
  Planarity :  0.004   0.045   1615
  Dihedral  :  8.575 158.008   1350
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 15.50 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.67 (0.23), residues: 1186
  helix: -0.49 (0.19), residues: 764
  sheet: -1.57 (0.69), residues: 56
  loop : -2.16 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   7 
 TYR   0.009   0.001   TYR A  13 
 PHE   0.010   0.001   PHE B 509 
 TRP   0.009   0.001   TRP A  15 
 HIS   0.002   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9286)
  covalent geometry    : angle       0.62160 (12653)
  hydrogen bonds       : bond        0.03532 (  438)
  hydrogen bonds       : angle       4.28394 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.7346 (mptm) cc_final: 0.7134 (mmtp)
REVERT: A   81 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7111 (ttp-170)
REVERT: A  148 PHE cc_start: 0.8134 (m-80) cc_final: 0.7828 (m-80)
REVERT: A  170 LEU cc_start: 0.7934 (tt) cc_final: 0.7641 (mt)
REVERT: A  195 ARG cc_start: 0.7562 (ttm170) cc_final: 0.6812 (tpp-160)
REVERT: A  282 MET cc_start: 0.7862 (tpp) cc_final: 0.7581 (mmt)
REVERT: A  392 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7386 (mm)
REVERT: A  409 SER cc_start: 0.8718 (t) cc_final: 0.8044 (p)
REVERT: A  487 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7383 (pp)
REVERT: A  509 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7420 (mtp85)
REVERT: B   26 ARG cc_start: 0.8253 (ptm160) cc_final: 0.7962 (ptm160)
REVERT: B   32 ARG cc_start: 0.6360 (pmt100) cc_final: 0.5081 (ptm-80)
REVERT: B  194 GLN cc_start: 0.6607 (tt0) cc_final: 0.6064 (tm-30)
REVERT: B  232 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6533 (ptt180)
REVERT: B  236 ARG cc_start: 0.7404 (ptm-80) cc_final: 0.6903 (mtm110)
REVERT: B  272 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7087 (mtp85)
REVERT: B  273 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7952 (mp0)
REVERT: B  284 SER cc_start: 0.8151 (p) cc_final: 0.7940 (m)
REVERT: B  304 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8628 (p)
REVERT: B  347 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5494 (tp)
REVERT: B  392 GLU cc_start: 0.7792 (tt0) cc_final: 0.6501 (tp30)
REVERT: B  394 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7252 (mt-10)
REVERT: B  498 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7210 (mp)
REVERT: B  578 THR cc_start: 0.8486 (t) cc_final: 0.8254 (m)
REVERT: B  590 ARG cc_start: 0.8093 (ptt90) cc_final: 0.7423 (ptt-90)
REVERT: B  602 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7270 (ptm160)
  outliers start: 44
  outliers final: 26
  residues processed: 178
  average time/residue: 0.5714
  time to fit residues: 108.6867
Evaluate side-chains
  170 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  273 GLU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 90 optimal weight:    0.4980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.138065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.109150 restraints weight = 10840.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.77
r_work: 0.3056 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9286  Z= 0.149
  Angle     :  0.632  14.364  12653  Z= 0.320
  Chirality :  0.043   0.173   1521
  Planarity :  0.004   0.045   1615
  Dihedral  :  8.478 155.819   1350
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 16.65 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.47 (0.23), residues: 1186
  helix: -0.35 (0.19), residues: 764
  sheet: -1.06 (0.72), residues: 51
  loop : -2.11 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 382 
 TYR   0.016   0.001   TYR A   9 
 PHE   0.012   0.001   PHE B 509 
 TRP   0.009   0.001   TRP A  15 
 HIS   0.003   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9286)
  covalent geometry    : angle       0.63190 (12653)
  hydrogen bonds       : bond        0.03627 (  438)
  hydrogen bonds       : angle       4.30358 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 140
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   81 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7685 (ttp-170)
REVERT: A  170 LEU cc_start: 0.8267 (tt) cc_final: 0.8016 (mt)
REVERT: A  195 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7500 (tpp-160)
REVERT: A  282 MET cc_start: 0.8252 (tpp) cc_final: 0.7998 (mmt)
REVERT: A  307 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8527 (mtt180)
REVERT: A  392 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7885 (mm)
REVERT: A  409 SER cc_start: 0.9024 (t) cc_final: 0.8415 (p)
REVERT: A  487 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7846 (pp)
REVERT: A  509 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7706 (mtp85)
REVERT: B   26 ARG cc_start: 0.8477 (ptm160) cc_final: 0.8248 (ptm160)
REVERT: B   32 ARG cc_start: 0.6758 (pmt100) cc_final: 0.5512 (ptm-80)
REVERT: B  194 GLN cc_start: 0.6878 (tt0) cc_final: 0.6570 (tm-30)
REVERT: B  232 ARG cc_start: 0.7479 (ttp80) cc_final: 0.6963 (ptt180)
REVERT: B  236 ARG cc_start: 0.7664 (ptm-80) cc_final: 0.7269 (mtm110)
REVERT: B  272 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7389 (mtp85)
REVERT: B  273 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8186 (mp0)
REVERT: B  304 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8813 (p)
REVERT: B  347 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5703 (tp)
REVERT: B  392 GLU cc_start: 0.8155 (tt0) cc_final: 0.7035 (tp30)
REVERT: B  394 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7531 (mt-10)
REVERT: B  498 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7790 (mp)
REVERT: B  578 THR cc_start: 0.8899 (t) cc_final: 0.8573 (m)
REVERT: B  586 LEU cc_start: 0.8755 (pp) cc_final: 0.8491 (pp)
REVERT: B  590 ARG cc_start: 0.8248 (ptt90) cc_final: 0.7702 (ptt-90)
REVERT: B  602 ARG cc_start: 0.8048 (ptp-170) cc_final: 0.7712 (ptm160)
  outliers start: 44
  outliers final: 27
  residues processed: 173
  average time/residue: 0.5662
  time to fit residues: 105.0620
Evaluate side-chains
  165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  273 GLU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  498 ILE
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0030
   chunk 97 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.4128

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
A 320 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.141326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.112726 restraints weight = 10664.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.75
r_work: 0.3052 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9286  Z= 0.112
  Angle     :  0.603  15.495  12653  Z= 0.303
  Chirality :  0.041   0.161   1521
  Planarity :  0.004   0.044   1615
  Dihedral  :  8.236 153.256   1350
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.59 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.07 (0.24), residues: 1186
  helix: -0.06 (0.19), residues: 774
  sheet: -1.06 (0.71), residues: 51
  loop : -1.93 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 382 
 TYR   0.009   0.001   TYR A   9 
 PHE   0.009   0.001   PHE B 336 
 TRP   0.010   0.001   TRP A  15 
 HIS   0.002   0.000   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9286)
  covalent geometry    : angle       0.60275 (12653)
  hydrogen bonds       : bond        0.03230 (  438)
  hydrogen bonds       : angle       4.16935 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   81 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7608 (ttp-170)
REVERT: A  148 PHE cc_start: 0.8448 (m-80) cc_final: 0.8177 (m-80)
REVERT: A  195 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7398 (tpp-160)
REVERT: A  282 MET cc_start: 0.8204 (tpp) cc_final: 0.7969 (mmt)
REVERT: A  392 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7785 (mm)
REVERT: A  409 SER cc_start: 0.8951 (t) cc_final: 0.8345 (p)
REVERT: A  487 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7746 (pp)
REVERT: A  509 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7652 (mtp85)
REVERT: B   26 ARG cc_start: 0.8433 (ptm160) cc_final: 0.8178 (ptm160)
REVERT: B   32 ARG cc_start: 0.6737 (pmt100) cc_final: 0.5494 (ptm-80)
REVERT: B   79 GLU cc_start: 0.8088 (mp0) cc_final: 0.7857 (mp0)
REVERT: B  106 GLN cc_start: 0.8241 (pt0) cc_final: 0.7891 (pm20)
REVERT: B  236 ARG cc_start: 0.7614 (ptm-80) cc_final: 0.7276 (ttm170)
REVERT: B  272 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7325 (mtp85)
REVERT: B  347 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.5683 (tp)
REVERT: B  392 GLU cc_start: 0.8071 (tt0) cc_final: 0.6930 (tp30)
REVERT: B  394 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7538 (mt-10)
REVERT: B  442 ASP cc_start: 0.8382 (m-30) cc_final: 0.7905 (OUTLIER)
REVERT: B  578 THR cc_start: 0.8777 (t) cc_final: 0.8506 (m)
REVERT: B  586 LEU cc_start: 0.8519 (pp) cc_final: 0.8270 (pp)
REVERT: B  590 ARG cc_start: 0.8172 (ptt90) cc_final: 0.7608 (ptt-90)
REVERT: B  602 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7631 (ptm160)
  outliers start: 39
  outliers final: 27
  residues processed: 174
  average time/residue: 0.5754
  time to fit residues: 107.2808
Evaluate side-chains
  166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  358 GLN
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  496 GLU
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 98 optimal weight:    0.0670
   chunk 42 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 187 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.142064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.113300 restraints weight = 10582.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.75
r_work: 0.2936 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9286  Z= 0.119
  Angle     :  0.607  15.818  12653  Z= 0.304
  Chirality :  0.042   0.160   1521
  Planarity :  0.004   0.044   1615
  Dihedral  :  8.019 150.166   1350
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.95 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.79 (0.24), residues: 1186
  helix:  0.19 (0.19), residues: 769
  sheet: -1.04 (0.70), residues: 51
  loop : -1.86 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 382 
 TYR   0.016   0.001   TYR A   9 
 PHE   0.010   0.001   PHE B 336 
 TRP   0.008   0.001   TRP A  15 
 HIS   0.002   0.001   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9286)
  covalent geometry    : angle       0.60681 (12653)
  hydrogen bonds       : bond        0.03284 (  438)
  hydrogen bonds       : angle       4.15670 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   81 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7171 (ttp-170)
REVERT: A  127 GLN cc_start: 0.8484 (tt0) cc_final: 0.8282 (pt0)
REVERT: A  148 PHE cc_start: 0.8198 (m-80) cc_final: 0.7929 (m-80)
REVERT: A  195 ARG cc_start: 0.7591 (ttm170) cc_final: 0.6840 (tpp-160)
REVERT: A  360 ARG cc_start: 0.7229 (ttm-80) cc_final: 0.6908 (ttm110)
REVERT: A  392 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7333 (mm)
REVERT: A  409 SER cc_start: 0.8742 (t) cc_final: 0.8066 (p)
REVERT: A  487 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7473 (pp)
REVERT: A  509 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7419 (mtp85)
REVERT: B   26 ARG cc_start: 0.8240 (ptm160) cc_final: 0.7956 (ptm160)
REVERT: B   32 ARG cc_start: 0.6422 (pmt100) cc_final: 0.5137 (ptm-80)
REVERT: B   79 GLU cc_start: 0.8059 (mp0) cc_final: 0.7761 (mp0)
REVERT: B  106 GLN cc_start: 0.8191 (pt0) cc_final: 0.7767 (pm20)
REVERT: B  236 ARG cc_start: 0.7421 (ptm-80) cc_final: 0.7025 (mtm110)
REVERT: B  272 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7129 (mtp85)
REVERT: B  347 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5463 (tp)
REVERT: B  392 GLU cc_start: 0.7787 (tt0) cc_final: 0.6518 (tp30)
REVERT: B  394 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: B  461 GLU cc_start: 0.7820 (mp0) cc_final: 0.7112 (tm-30)
REVERT: B  578 THR cc_start: 0.8574 (t) cc_final: 0.8260 (m)
REVERT: B  586 LEU cc_start: 0.8259 (pp) cc_final: 0.7982 (pp)
REVERT: B  590 ARG cc_start: 0.8075 (ptt90) cc_final: 0.7445 (ptt-90)
REVERT: B  602 ARG cc_start: 0.7669 (ptp-170) cc_final: 0.7291 (ptm160)
REVERT: B  621 GLU cc_start: 0.7835 (pt0) cc_final: 0.7512 (pt0)
  outliers start: 34
  outliers final: 23
  residues processed: 163
  average time/residue: 0.6024
  time to fit residues: 105.1525
Evaluate side-chains
  163 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  622 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 88 optimal weight:    0.4980
   chunk 104 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 187 GLN
A 320 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.140771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.111688 restraints weight = 10649.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.77
r_work: 0.2917 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9286  Z= 0.138
  Angle     :  0.629  15.733  12653  Z= 0.314
  Chirality :  0.043   0.163   1521
  Planarity :  0.004   0.044   1615
  Dihedral  :  7.831 148.336   1350
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.16 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.72 (0.24), residues: 1186
  helix:  0.25 (0.19), residues: 768
  sheet: -1.01 (0.71), residues: 51
  loop : -1.83 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 382 
 TYR   0.015   0.001   TYR A   9 
 PHE   0.010   0.001   PHE B 509 
 TRP   0.010   0.001   TRP A  15 
 HIS   0.002   0.001   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9286)
  covalent geometry    : angle       0.62910 (12653)
  hydrogen bonds       : bond        0.03469 (  438)
  hydrogen bonds       : angle       4.18977 ( 1293)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   81 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7149 (ttp-170)
REVERT: A  127 GLN cc_start: 0.8480 (tt0) cc_final: 0.8241 (pt0)
REVERT: A  148 PHE cc_start: 0.8171 (m-80) cc_final: 0.7908 (m-80)
REVERT: A  195 ARG cc_start: 0.7621 (ttm170) cc_final: 0.6810 (tpp-160)
REVERT: A  282 MET cc_start: 0.8018 (mpp) cc_final: 0.7808 (mmt)
REVERT: A  392 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7317 (mm)
REVERT: A  409 SER cc_start: 0.8727 (t) cc_final: 0.8046 (p)
REVERT: A  487 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7462 (pp)
REVERT: A  509 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7363 (mtp85)
REVERT: B   26 ARG cc_start: 0.8260 (ptm160) cc_final: 0.7974 (ptm160)
REVERT: B   32 ARG cc_start: 0.6462 (pmt100) cc_final: 0.5167 (ptm-80)
REVERT: B   79 GLU cc_start: 0.8035 (mp0) cc_final: 0.7713 (mp0)
REVERT: B  106 GLN cc_start: 0.8216 (pt0) cc_final: 0.7766 (pm20)
REVERT: B  162 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8029 (mm)
REVERT: B  236 ARG cc_start: 0.7421 (ptm-80) cc_final: 0.6955 (ttm170)
REVERT: B  272 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7136 (mtp85)
REVERT: B  347 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5438 (tp)
REVERT: B  392 GLU cc_start: 0.7779 (tt0) cc_final: 0.6504 (tp30)
REVERT: B  394 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7279 (mt-10)
REVERT: B  461 GLU cc_start: 0.7804 (mp0) cc_final: 0.7084 (tm-30)
REVERT: B  578 THR cc_start: 0.8566 (t) cc_final: 0.8196 (m)
REVERT: B  586 LEU cc_start: 0.8222 (pp) cc_final: 0.7931 (pp)
REVERT: B  590 ARG cc_start: 0.8132 (ptt90) cc_final: 0.7500 (ptt-90)
REVERT: B  602 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.7244 (ptm160)
REVERT: B  621 GLU cc_start: 0.7827 (pt0) cc_final: 0.7340 (tm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 163
  average time/residue: 0.6117
  time to fit residues: 106.6595
Evaluate side-chains
  167 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  622 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0270
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0870
   chunk 8 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 187 GLN
A 320 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.143205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.114546 restraints weight = 10564.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.75
r_work: 0.3114 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   9286  Z= 0.108
  Angle     :  0.609  15.837  12653  Z= 0.300
  Chirality :  0.041   0.152   1521
  Planarity :  0.004   0.043   1615
  Dihedral  :  7.302 146.073   1350
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.79 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.41 (0.24), residues: 1186
  helix:  0.49 (0.19), residues: 768
  sheet: -0.95 (0.71), residues: 51
  loop : -1.69 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 382 
 TYR   0.011   0.001   TYR A   9 
 PHE   0.008   0.001   PHE A 453 
 TRP   0.010   0.001   TRP A  15 
 HIS   0.002   0.001   HIS B 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9286)
  covalent geometry    : angle       0.60915 (12653)
  hydrogen bonds       : bond        0.03077 (  438)
  hydrogen bonds       : angle       4.06920 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3675.22 seconds
wall clock time: 63 minutes 16.30 seconds (3796.30 seconds total)