Starting phenix.real_space_refine
on Wed Sep 17 19:42:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hrb_0258/09_2025/6hrb_0258.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hrb_0258/09_2025/6hrb_0258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hrb_0258/09_2025/6hrb_0258.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hrb_0258/09_2025/6hrb_0258.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hrb_0258/09_2025/6hrb_0258.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hrb_0258/09_2025/6hrb_0258.map"
  }
  resolution = 4.0
  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=   0.008
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
     K       1      8.98       5
     P       1      5.49       5
     S      61      5.16       5
     C    6947      2.51       5
     N    1818      2.21       5
     O    1959      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  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: 10787
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "B"
      Number of atoms: 5008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5008
          Classifications: {'peptide': 674}
          Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 646}
    Chain: "C"
      Number of atoms: 1423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1423
          Classifications: {'peptide': 189}
          Link IDs: {'PTRANS': 13, 'TRANS': 175}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.49, per 1000 atoms: 0.23
  Number of scatterers: 10787
  At special positions: 0
  Unit cell: (88.044, 114.356, 161.92, 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)
     K       1     19.00
     S      61     16.00
     P       1     15.00
     O    1959      8.00
     N    1818      7.00
     C    6947      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: 0.92
  Conformation dependent library (CDL) restraints added in 403.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2632

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 10 sheets defined
      60.7% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 32
      removed outlier: 3.548A  pdb=" N   ILE A   9 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
      Proline residue:  A  22  - end of helix
      removed outlier: 4.116A  pdb=" N   ARG A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 51
      removed outlier: 3.626A  pdb=" N   ARG A  44 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 81
      removed outlier: 3.597A  pdb=" N   CYS A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
      removed outlier: 4.687A  pdb=" N   HIS A  85 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 111
      removed outlier: 3.853A  pdb=" N   VAL A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 133 through 157
      removed outlier: 3.866A  pdb=" N   PHE A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 142 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 177 through 192
      removed outlier: 3.529A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.603A  pdb=" N   ALA A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   MET A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 260
      removed outlier: 3.845A  pdb=" N   PHE A 260 " --> pdb=" O   MET A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 274
      removed outlier: 3.545A  pdb=" N   THR A 264 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   CYS A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 284
    Processing helix  chain 'A' and resid 284 through 305
      removed outlier: 3.613A  pdb=" N   VAL A 289 " --> pdb=" O   TRP A 285 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   ILE A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL A 298 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 313
      removed outlier: 4.421A  pdb=" N   LEU A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
      removed outlier: 3.556A  pdb=" N   VAL A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   THR A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 355 through 368
      Proline residue:  A 362  - end of helix
      removed outlier: 3.546A  pdb=" N   GLN A 367 " --> pdb=" O   MET A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 399
      removed outlier: 3.893A  pdb=" N   PHE A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 421
      removed outlier: 4.027A  pdb=" N   LEU A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   THR A 417 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 428
      removed outlier: 4.009A  pdb=" N   VAL A 428 " --> pdb=" O   THR A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 438
      removed outlier: 3.756A  pdb=" N   THR A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.780A  pdb=" N   MET A 445 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 462
      removed outlier: 3.805A  pdb=" N   PHE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL A 456 " --> pdb=" O   GLY A 452 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ALA A 459 " --> pdb=" O   GLU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 495
      removed outlier: 3.856A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 507
    Processing helix  chain 'A' and resid 524 through 549
      removed outlier: 3.729A  pdb=" N   GLY A 529 " --> pdb=" O   PRO A 525 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 533 " --> pdb=" O   GLY A 529 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU A 537 " --> pdb=" O   GLY A 533 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      Proline residue:  A 545  - end of helix
      removed outlier: 3.749A  pdb=" N   LEU A 549 " --> pdb=" O   PRO A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'B' and resid 11 through 24
      removed outlier: 3.558A  pdb=" N   ALA B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS B  19 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLU B  20 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ALA B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 56
      removed outlier: 3.843A  pdb=" N   ILE B  38 " --> pdb=" O   PRO B  34 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR B  47 " --> pdb=" O   SER B  43 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 87
      removed outlier: 3.626A  pdb=" N   SER B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TRP B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU B  72 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 103
      removed outlier: 3.618A  pdb=" N   VAL B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LYS B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 208
      removed outlier: 4.033A  pdb=" N   MET B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 238
      removed outlier: 3.578A  pdb=" N   LEU B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR B 222 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE B 223 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU B 224 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   THR B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   VAL B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 244
    Processing helix  chain 'B' and resid 251 through 263
      removed outlier: 3.672A  pdb=" N   ALA B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ILE B 263 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 274 through 283
      removed outlier: 3.619A  pdb=" N   GLY B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU B 283 " --> pdb=" O   MET B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 297
      removed outlier: 3.707A  pdb=" N   GLU B 296 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 300
      No H-bonds generated for 'chain 'B' and resid 298 through 300'
    Processing helix  chain 'B' and resid 329 through 340
      removed outlier: 3.732A  pdb=" N   LEU B 333 " --> pdb=" O   ASP B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 357
      removed outlier: 4.023A  pdb=" N   ILE B 352 " --> pdb=" O   GLU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 408
      removed outlier: 3.904A  pdb=" N   ILE B 401 " --> pdb=" O   SER B 397 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS B 404 " --> pdb=" O   ALA B 400 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU B 406 " --> pdb=" O   ARG B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 424
      removed outlier: 4.008A  pdb=" N   ASP B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 463
      removed outlier: 3.600A  pdb=" N   GLN B 459 " --> pdb=" O   GLU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 484
      removed outlier: 4.472A  pdb=" N   ALA B 480 " --> pdb=" O   LEU B 476 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE B 481 " --> pdb=" O   THR B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 507
      removed outlier: 3.525A  pdb=" N   LYS B 499 " --> pdb=" O   THR B 495 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B 500 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 526
      removed outlier: 4.502A  pdb=" N   ALA B 525 " --> pdb=" O   ASN B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 546
    Processing helix  chain 'B' and resid 557 through 591
      removed outlier: 3.740A  pdb=" N   VAL B 561 " --> pdb=" O   LYS B 557 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN B 567 " --> pdb=" O   HIS B 563 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   SER B 574 " --> pdb=" O   MET B 570 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA B 581 " --> pdb=" O   THR B 577 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   VAL B 584 " --> pdb=" O   ILE B 580 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B 588 " --> pdb=" O   VAL B 584 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA B 589 " --> pdb=" O   ALA B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 596
      removed outlier: 3.677A  pdb=" N   PHE B 595 " --> pdb=" O   PRO B 592 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA B 596 " --> pdb=" O   ALA B 593 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 592 through 596'
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 3.917A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 637
      removed outlier: 3.706A  pdb=" N   ILE B 617 " --> pdb=" O   PRO B 613 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B 618 " --> pdb=" O   ASP B 614 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ILE B 632 " --> pdb=" O   ILE B 628 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 646 through 657
      removed outlier: 3.939A  pdb=" N   LEU B 650 " --> pdb=" O   ALA B 646 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TRP B 655 " --> pdb=" O   ARG B 651 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 656 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 679
      removed outlier: 3.546A  pdb=" N   LEU B 662 " --> pdb=" O   GLY B 658 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 664 " --> pdb=" O   GLY B 660 " (cutoff:3.500A)
      Proline residue:  B 665  - end of helix
      removed outlier: 3.868A  pdb=" N   LYS B 670 " --> pdb=" O   PHE B 666 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU B 674 " --> pdb=" O   LYS B 670 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   CYS B 679 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 19
      removed outlier: 3.789A  pdb=" N   THR C  10 " --> pdb=" O   PRO C   6 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   PHE C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 34
      removed outlier: 4.339A  pdb=" N   LEU C  24 " --> pdb=" O   GLY C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 40
      removed outlier: 3.523A  pdb=" N   ALA C  38 " --> pdb=" O   PHE C  34 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN C  39 " --> pdb=" O   PRO C  35 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY C  40 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 34 through 40'
    Processing helix  chain 'C' and resid 91 through 109
      removed outlier: 3.896A  pdb=" N   ASP C  95 " --> pdb=" O   ASN C  91 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA C 103 " --> pdb=" O   ALA C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 122
      removed outlier: 3.768A  pdb=" N   VAL C 121 " --> pdb=" O   PRO C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 140
    Processing helix  chain 'C' and resid 140 through 149
      removed outlier: 3.763A  pdb=" N   VAL C 144 " --> pdb=" O   GLN C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 178 through 188
    Processing helix  chain 'D' and resid 6 through 25
      removed outlier: 4.126A  pdb=" N   TYR D  21 " --> pdb=" O   GLY D  17 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASN D  25 " --> pdb=" O   TYR D  21 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205
      removed outlier: 3.527A  pdb=" N   GLN A 212 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 109
    Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134
      removed outlier: 6.735A  pdb=" N   GLU B 190 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   VAL B 146 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 168
    Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289
      removed outlier: 3.910A  pdb=" N   ASP B 550 " --> pdb=" O   ALA B 534 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491
      removed outlier: 6.820A  pdb=" N   THR B 467 " --> pdb=" O   ASP B 489 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   LEU B 491 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   MET B 469 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   LEU B 304 " --> pdb=" O   VAL B 468 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE B 470 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   LEU B 306 " --> pdb=" O   ILE B 470 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   VAL B 303 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   THR B 516 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   LEU B 305 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 373 through 375
      removed outlier: 3.810A  pdb=" N   GLY B 441 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLU B 435 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   VAL B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 45
      removed outlier: 5.706A  pdb=" N   ILE C  43 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 132

    523 hydrogen bonds defined for protein.
    1515 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: 1.91

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3441
        1.34 -     1.46: 1833
        1.46 -     1.57: 5598
        1.57 -     1.69: 4
        1.69 -     1.81: 110
  Bond restraints: 10986
  Sorted by residual:
  bond pdb=" N   ARG B  89 "
       pdb=" CA  ARG B  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.502 -0.044 1.90e-02 2.77e+03 5.25e+00
  bond pdb=" CB  VAL A 428 "
       pdb=" CG2 VAL A 428 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.70e+00
  bond pdb=" C   LEU A 213 "
       pdb=" N   LEU A 214 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 2.07e-02 2.33e+03 3.19e+00
  bond pdb=" CA  ARG B  89 "
       pdb=" CB  ARG B  89 "
    ideal  model  delta    sigma   weight residual
    1.530  1.565 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C   GLN C 164 "
       pdb=" N   GLN C 165 "
    ideal  model  delta    sigma   weight residual
    1.331  1.283  0.048 2.83e-02 1.25e+03 2.92e+00
  ... (remaining 10981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 14668
        2.82 -     5.63: 241
        5.63 -     8.45: 36
        8.45 -    11.26: 6
       11.26 -    14.08: 3
  Bond angle restraints: 14954
  Sorted by residual:
  angle pdb=" C   GLY B  88 "
        pdb=" N   ARG B  89 "
        pdb=" CA  ARG B  89 "
      ideal   model   delta    sigma   weight residual
     121.70  135.78  -14.08 1.80e+00 3.09e-01 6.12e+01
  angle pdb=" C   MET A 360 "
        pdb=" N   VAL A 361 "
        pdb=" CA  VAL A 361 "
      ideal   model   delta    sigma   weight residual
     120.24  124.03   -3.79 6.30e-01 2.52e+00 3.61e+01
  angle pdb=" N   ASN B  26 "
        pdb=" CA  ASN B  26 "
        pdb=" C   ASN B  26 "
      ideal   model   delta    sigma   weight residual
     109.81  119.59   -9.78 2.21e+00 2.05e-01 1.96e+01
  angle pdb=" C   ALA B 319 "
        pdb=" N   SER B 320 "
        pdb=" CA  SER B 320 "
      ideal   model   delta    sigma   weight residual
     121.54  129.41   -7.87 1.91e+00 2.74e-01 1.70e+01
  angle pdb=" CB  LEU A 133 "
        pdb=" CG  LEU A 133 "
        pdb=" CD2 LEU A 133 "
      ideal   model   delta    sigma   weight residual
     110.70   98.39   12.31 3.00e+00 1.11e-01 1.68e+01
  ... (remaining 14949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.50: 6245
       15.50 -    31.01: 244
       31.01 -    46.51: 36
       46.51 -    62.01: 5
       62.01 -    77.51: 3
  Dihedral angle restraints: 6533
    sinusoidal: 2436
      harmonic: 4097
  Sorted by residual:
  dihedral pdb=" CA  ASN A 239 "
           pdb=" C   ASN A 239 "
           pdb=" N   SER A 240 "
           pdb=" CA  SER A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.70   31.30     0      5.00e+00 4.00e-02 3.92e+01
  dihedral pdb=" CA  ALA B 319 "
           pdb=" C   ALA B 319 "
           pdb=" N   SER B 320 "
           pdb=" CA  SER B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.18   29.82     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  ALA A 238 "
           pdb=" C   ALA A 238 "
           pdb=" N   ASN A 239 "
           pdb=" CA  ASN A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.31  -28.69     0      5.00e+00 4.00e-02 3.29e+01
  ... (remaining 6530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1144
       0.046 -    0.092: 499
       0.092 -    0.138: 138
       0.138 -    0.185: 16
       0.185 -    0.231: 6
  Chirality restraints: 1803
  Sorted by residual:
  chirality pdb=" CA  ARG B  89 "
            pdb=" N   ARG B  89 "
            pdb=" C   ARG B  89 "
            pdb=" CB  ARG B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE B 388 "
            pdb=" CA  ILE B 388 "
            pdb=" CG1 ILE B 388 "
            pdb=" CG2 ILE B 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  VAL B 449 "
            pdb=" CA  VAL B 449 "
            pdb=" CG1 VAL B 449 "
            pdb=" CG2 VAL B 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1800 not shown)

  Planarity restraints: 1898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 424 "   -0.058 5.00e-02 4.00e+02   8.67e-02 1.20e+01
        pdb=" N   PRO A 425 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 425 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 425 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 240 "   -0.041 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO B 241 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 523 "   -0.040 5.00e-02 4.00e+02   6.02e-02 5.81e+00
        pdb=" N   PRO B 524 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 524 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 524 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1895 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.78: 2659
        2.78 -     3.37: 12152
        3.37 -     3.96: 20687
        3.96 -     4.55: 29120
        4.55 -     5.14: 41922
  Nonbonded interactions: 106540
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 307 "
            pdb=" OG1 THR B 311 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OG1 THR C  72 "
            pdb=" O   MET C  75 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   VAL A 107 "
            pdb=" OG1 THR A 111 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OG  SER A 343 "
            pdb=" O   ASN A 466 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   MET A 130 "
            pdb=" OG1 THR A 134 "
     model   vdw
     2.264 3.040
  ... (remaining 106535 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
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      :  0.008   0.085  10986  Z= 0.337
  Angle     :  0.963  14.078  14954  Z= 0.499
  Chirality :  0.054   0.231   1803
  Planarity :  0.007   0.087   1898
  Dihedral  :  9.280  77.514   3901
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.50 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -4.97 (0.16), residues: 1436
  helix: -3.80 (0.10), residues: 765
  sheet: -2.20 (0.46), residues: 91
  loop : -2.48 (0.22), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 172 
 TYR   0.015   0.003   TYR A 201 
 PHE   0.025   0.003   PHE A 471 
 TRP   0.024   0.002   TRP B 245 
 HIS   0.012   0.002   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 (10986)
  covalent geometry    : angle       0.96308 (14954)
  hydrogen bonds       : bond        0.29646 (  523)
  hydrogen bonds       : angle      10.20594 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 240
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.8870 (p0) cc_final: 0.8537 (p0)
REVERT: A  167 TRP cc_start: 0.8897 (m100) cc_final: 0.8258 (m100)
REVERT: A  175 LEU cc_start: 0.9369 (mt) cc_final: 0.8536 (tp)
REVERT: A  227 MET cc_start: 0.8998 (mmm) cc_final: 0.8195 (mmt)
REVERT: A  287 MET cc_start: 0.9044 (mtm) cc_final: 0.8481 (mtp)
REVERT: A  320 MET cc_start: 0.8796 (mmm) cc_final: 0.8336 (tpp)
REVERT: A  366 MET cc_start: 0.9280 (mtm) cc_final: 0.8999 (mtm)
REVERT: A  392 PHE cc_start: 0.8360 (t80) cc_final: 0.7865 (t80)
REVERT: A  469 SER cc_start: 0.9426 (m) cc_final: 0.8875 (p)
REVERT: A  510 LYS cc_start: 0.8642 (mttm) cc_final: 0.8434 (mtpt)
REVERT: A  537 LEU cc_start: 0.8895 (tp) cc_final: 0.8646 (tp)
REVERT: A  541 LEU cc_start: 0.9595 (mt) cc_final: 0.9295 (mp)
REVERT: B  371 HIS cc_start: 0.8348 (m-70) cc_final: 0.8106 (m-70)
REVERT: C   22 TYR cc_start: 0.9150 (t80) cc_final: 0.8749 (t80)
REVERT: C   48 THR cc_start: 0.9290 (p) cc_final: 0.8427 (p)
REVERT: D   14 LEU cc_start: 0.9444 (mt) cc_final: 0.9117 (tt)
REVERT: D   21 TYR cc_start: 0.9335 (t80) cc_final: 0.8894 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 242
  average time/residue: 0.0967
  time to fit residues: 33.4974
Evaluate side-chains
  126 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0870
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 HIS
A 466 ASN
B 316 ASN
B 326 GLN
B 404 HIS
B 536 ASN
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 624 ASN
C  31 GLN
C 154 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.058654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.047921 restraints weight = 50078.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.049360 restraints weight = 24567.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.050321 restraints weight = 14731.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.050953 restraints weight = 10137.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.051400 restraints weight = 7655.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10986  Z= 0.158
  Angle     :  0.693   9.657  14954  Z= 0.352
  Chirality :  0.042   0.197   1803
  Planarity :  0.005   0.049   1898
  Dihedral  :  5.626  24.176   1525
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.27 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.12 (0.19), residues: 1436
  helix: -1.90 (0.15), residues: 820
  sheet: -1.94 (0.44), residues: 104
  loop : -2.07 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 359 
 TYR   0.021   0.001   TYR A 381 
 PHE   0.018   0.002   PHE C  13 
 TRP   0.017   0.001   TRP A 176 
 HIS   0.002   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10986)
  covalent geometry    : angle       0.69284 (14954)
  hydrogen bonds       : bond        0.05036 (  523)
  hydrogen bonds       : angle       5.55470 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.8811 (p0) cc_final: 0.8239 (p0)
REVERT: A  167 TRP cc_start: 0.8865 (m100) cc_final: 0.8298 (m100)
REVERT: A  176 TRP cc_start: 0.8025 (m100) cc_final: 0.7065 (m100)
REVERT: A  392 PHE cc_start: 0.8402 (t80) cc_final: 0.7863 (t80)
REVERT: A  489 MET cc_start: 0.9210 (mtm) cc_final: 0.8825 (mtm)
REVERT: A  537 LEU cc_start: 0.8906 (tp) cc_final: 0.8566 (tp)
REVERT: A  541 LEU cc_start: 0.9616 (mt) cc_final: 0.9351 (mp)
REVERT: B  383 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7449 (mtm)
REVERT: C   10 THR cc_start: 0.9278 (m) cc_final: 0.8937 (m)
REVERT: C   50 ARG cc_start: 0.7997 (mmt180) cc_final: 0.7740 (mtt-85)
REVERT: C   74 GLU cc_start: 0.7916 (tp30) cc_final: 0.7549 (tp30)
REVERT: C  129 ASP cc_start: 0.8428 (t0) cc_final: 0.8222 (t0)
  outliers start: 23
  outliers final: 8
  residues processed: 181
  average time/residue: 0.0815
  time to fit residues: 22.6667
Evaluate side-chains
  130 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain D residue    9 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 123 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 GLN
B 547 ASN
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.056051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.045200 restraints weight = 51382.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.046581 restraints weight = 25507.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.047397 restraints weight = 15350.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.048113 restraints weight = 10999.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.048537 restraints weight = 8207.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  10986  Z= 0.249
  Angle     :  0.741   8.968  14954  Z= 0.370
  Chirality :  0.044   0.200   1803
  Planarity :  0.004   0.047   1898
  Dihedral  :  5.320  24.147   1524
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.65 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.21), residues: 1436
  helix: -0.90 (0.17), residues: 828
  sheet: -1.79 (0.44), residues: 107
  loop : -1.92 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  68 
 TYR   0.015   0.002   TYR A 381 
 PHE   0.021   0.002   PHE A 138 
 TRP   0.011   0.002   TRP A 176 
 HIS   0.005   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (10986)
  covalent geometry    : angle       0.74144 (14954)
  hydrogen bonds       : bond        0.04052 (  523)
  hydrogen bonds       : angle       5.15360 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.9014 (p0) cc_final: 0.8447 (p0)
REVERT: A  176 TRP cc_start: 0.8195 (m100) cc_final: 0.7986 (m100)
REVERT: A  367 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8602 (mp10)
REVERT: A  383 MET cc_start: 0.9387 (tpp) cc_final: 0.9186 (tpp)
REVERT: A  392 PHE cc_start: 0.8323 (t80) cc_final: 0.7843 (t80)
REVERT: A  489 MET cc_start: 0.9237 (mtm) cc_final: 0.8990 (mtm)
REVERT: A  537 LEU cc_start: 0.9057 (tp) cc_final: 0.8745 (tp)
REVERT: A  541 LEU cc_start: 0.9618 (mt) cc_final: 0.9335 (mp)
REVERT: B  383 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7366 (mtm)
REVERT: C   75 MET cc_start: 0.8204 (pmm) cc_final: 0.7863 (pmm)
REVERT: C  129 ASP cc_start: 0.8419 (t0) cc_final: 0.8205 (t0)
  outliers start: 26
  outliers final: 16
  residues processed: 143
  average time/residue: 0.0751
  time to fit residues: 17.0013
Evaluate side-chains
  126 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  367 GLN
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain D residue    9 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 57 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9980
   chunk 101 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   chunk 117 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 135 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    2.8084

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 112 ASN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
A 231 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.056210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.045482 restraints weight = 51448.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.046877 restraints weight = 25338.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.047822 restraints weight = 15200.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.048427 restraints weight = 10438.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.048860 restraints weight = 7900.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10986  Z= 0.189
  Angle     :  0.667   9.069  14954  Z= 0.331
  Chirality :  0.042   0.160   1803
  Planarity :  0.003   0.047   1898
  Dihedral  :  5.049  23.681   1524
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.65 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.21), residues: 1436
  helix: -0.24 (0.17), residues: 829
  sheet: -1.54 (0.45), residues: 107
  loop : -1.85 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 157 
 TYR   0.018   0.002   TYR B 641 
 PHE   0.020   0.002   PHE A 260 
 TRP   0.012   0.001   TRP A 167 
 HIS   0.005   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (10986)
  covalent geometry    : angle       0.66674 (14954)
  hydrogen bonds       : bond        0.03516 (  523)
  hydrogen bonds       : angle       4.77710 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.9061 (p0) cc_final: 0.8446 (p0)
REVERT: A  256 MET cc_start: 0.8978 (mtp) cc_final: 0.8699 (mtt)
REVERT: A  350 MET cc_start: 0.8593 (mmm) cc_final: 0.8387 (mmm)
REVERT: A  392 PHE cc_start: 0.8326 (t80) cc_final: 0.7985 (t80)
REVERT: A  458 TYR cc_start: 0.9462 (t80) cc_final: 0.9154 (t80)
REVERT: A  489 MET cc_start: 0.9226 (mtm) cc_final: 0.8845 (mtm)
REVERT: A  537 LEU cc_start: 0.9029 (tp) cc_final: 0.8642 (tp)
REVERT: A  541 LEU cc_start: 0.9616 (mt) cc_final: 0.9307 (mp)
REVERT: B  221 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9075 (tt)
REVERT: B  383 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7327 (mtm)
REVERT: C   75 MET cc_start: 0.8360 (pmm) cc_final: 0.8092 (pmm)
  outliers start: 29
  outliers final: 17
  residues processed: 138
  average time/residue: 0.0749
  time to fit residues: 16.4939
Evaluate side-chains
  127 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain D residue    9 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 ASN
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.056564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.045910 restraints weight = 51069.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.047302 restraints weight = 25137.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.048259 restraints weight = 15128.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.048918 restraints weight = 10350.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.049258 restraints weight = 7744.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10986  Z= 0.159
  Angle     :  0.629   9.027  14954  Z= 0.313
  Chirality :  0.042   0.169   1803
  Planarity :  0.003   0.050   1898
  Dihedral  :  4.884  23.365   1524
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.44 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.99 (0.22), residues: 1436
  helix:  0.15 (0.18), residues: 832
  sheet: -1.38 (0.46), residues: 107
  loop : -1.76 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 425 
 TYR   0.014   0.002   TYR A 381 
 PHE   0.017   0.001   PHE A 260 
 TRP   0.034   0.001   TRP A 176 
 HIS   0.004   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (10986)
  covalent geometry    : angle       0.62903 (14954)
  hydrogen bonds       : bond        0.03326 (  523)
  hydrogen bonds       : angle       4.60539 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.9053 (p0) cc_final: 0.8395 (p0)
REVERT: A  256 MET cc_start: 0.8993 (mtp) cc_final: 0.8670 (mtt)
REVERT: A  392 PHE cc_start: 0.8332 (t80) cc_final: 0.8028 (t80)
REVERT: A  489 MET cc_start: 0.9188 (mtm) cc_final: 0.8778 (mtm)
REVERT: A  537 LEU cc_start: 0.9033 (tp) cc_final: 0.8623 (tp)
REVERT: A  541 LEU cc_start: 0.9607 (mt) cc_final: 0.9287 (mp)
REVERT: B  383 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7261 (mtm)
REVERT: C   22 TYR cc_start: 0.8994 (t80) cc_final: 0.8642 (t80)
REVERT: C   43 ILE cc_start: 0.8860 (mt) cc_final: 0.8635 (tt)
REVERT: C   75 MET cc_start: 0.8479 (pmm) cc_final: 0.8191 (pmm)
REVERT: C  180 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7940 (mm-30)
  outliers start: 25
  outliers final: 16
  residues processed: 140
  average time/residue: 0.0760
  time to fit residues: 16.8398
Evaluate side-chains
  125 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  437 MET
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain D residue    9 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 137 optimal weight:    0.0970
   chunk 123 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 55 optimal weight:    0.3980
   chunk 102 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 84 optimal weight:    5.9990
   chunk 130 optimal weight:   10.0000
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.058030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.047441 restraints weight = 50933.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.048868 restraints weight = 25064.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.049848 restraints weight = 15009.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.050484 restraints weight = 10231.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.050914 restraints weight = 7704.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10986  Z= 0.116
  Angle     :  0.607   9.096  14954  Z= 0.298
  Chirality :  0.040   0.148   1803
  Planarity :  0.003   0.050   1898
  Dihedral  :  4.724  25.196   1524
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.21 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.62 (0.22), residues: 1436
  helix:  0.47 (0.18), residues: 844
  sheet: -1.20 (0.47), residues: 106
  loop : -1.73 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 157 
 TYR   0.019   0.001   TYR B 641 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.025   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10986)
  covalent geometry    : angle       0.60731 (14954)
  hydrogen bonds       : bond        0.03134 (  523)
  hydrogen bonds       : angle       4.42058 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.8061 (p)
REVERT: A  100 ASP cc_start: 0.8996 (p0) cc_final: 0.8203 (p0)
REVERT: A  227 MET cc_start: 0.8171 (mmm) cc_final: 0.7899 (mmm)
REVERT: A  256 MET cc_start: 0.8924 (mtp) cc_final: 0.8722 (mtt)
REVERT: A  380 LEU cc_start: 0.9339 (tp) cc_final: 0.9014 (tp)
REVERT: A  537 LEU cc_start: 0.8984 (tp) cc_final: 0.8580 (tp)
REVERT: A  541 LEU cc_start: 0.9600 (mt) cc_final: 0.9273 (mp)
REVERT: B  383 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7236 (mtm)
REVERT: C   22 TYR cc_start: 0.8916 (t80) cc_final: 0.8669 (t80)
REVERT: C   24 LEU cc_start: 0.9297 (pp) cc_final: 0.8986 (mm)
REVERT: C   43 ILE cc_start: 0.8807 (mt) cc_final: 0.8523 (tt)
REVERT: C   75 MET cc_start: 0.8559 (pmm) cc_final: 0.8284 (pmm)
REVERT: C  180 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7920 (mm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 143
  average time/residue: 0.0797
  time to fit residues: 17.6997
Evaluate side-chains
  125 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue   10 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0670
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0270
   overall best weight:    0.5376

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.058725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.048300 restraints weight = 50260.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.049775 restraints weight = 24498.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.050702 restraints weight = 14464.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.051350 restraints weight = 9882.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.051634 restraints weight = 7414.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10986  Z= 0.113
  Angle     :  0.609   9.567  14954  Z= 0.299
  Chirality :  0.041   0.256   1803
  Planarity :  0.003   0.051   1898
  Dihedral  :  4.598  26.534   1524
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.80 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.42 (0.22), residues: 1436
  helix:  0.65 (0.18), residues: 846
  sheet: -1.03 (0.48), residues: 106
  loop : -1.72 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 281 
 TYR   0.024   0.002   TYR B 641 
 PHE   0.049   0.002   PHE C  13 
 TRP   0.028   0.001   TRP A 176 
 HIS   0.004   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10986)
  covalent geometry    : angle       0.60945 (14954)
  hydrogen bonds       : bond        0.03066 (  523)
  hydrogen bonds       : angle       4.34904 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.8987 (p0) cc_final: 0.8228 (p0)
REVERT: A  256 MET cc_start: 0.8999 (mtp) cc_final: 0.8736 (mtt)
REVERT: A  380 LEU cc_start: 0.9312 (tp) cc_final: 0.8994 (tp)
REVERT: A  426 THR cc_start: 0.8589 (m) cc_final: 0.8239 (m)
REVERT: A  439 ASP cc_start: 0.8387 (p0) cc_final: 0.8058 (t70)
REVERT: A  537 LEU cc_start: 0.8940 (tp) cc_final: 0.8580 (tp)
REVERT: B  383 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7223 (mtm)
REVERT: C   24 LEU cc_start: 0.9290 (pp) cc_final: 0.8984 (mm)
REVERT: C   75 MET cc_start: 0.8565 (pmm) cc_final: 0.8308 (pmm)
  outliers start: 17
  outliers final: 11
  residues processed: 147
  average time/residue: 0.0791
  time to fit residues: 18.0127
Evaluate side-chains
  130 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   73 TRP
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue   10 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   chunk 123 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 105 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 106 optimal weight:   50.0000
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.058411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.047871 restraints weight = 50527.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.049250 restraints weight = 24835.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.050178 restraints weight = 14959.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.050791 restraints weight = 10334.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.051269 restraints weight = 7824.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10986  Z= 0.125
  Angle     :  0.629  11.992  14954  Z= 0.306
  Chirality :  0.041   0.199   1803
  Planarity :  0.003   0.050   1898
  Dihedral  :  4.538  27.642   1524
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.98 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.26 (0.22), residues: 1436
  helix:  0.78 (0.18), residues: 847
  sheet: -0.90 (0.49), residues: 106
  loop : -1.67 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 153 
 TYR   0.026   0.002   TYR B 641 
 PHE   0.033   0.002   PHE C  13 
 TRP   0.031   0.001   TRP A 176 
 HIS   0.005   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10986)
  covalent geometry    : angle       0.62895 (14954)
  hydrogen bonds       : bond        0.03029 (  523)
  hydrogen bonds       : angle       4.29135 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.9015 (p0) cc_final: 0.8263 (p0)
REVERT: A  256 MET cc_start: 0.8984 (mtp) cc_final: 0.8765 (mtt)
REVERT: A  380 LEU cc_start: 0.9349 (tp) cc_final: 0.8797 (tp)
REVERT: A  426 THR cc_start: 0.8562 (m) cc_final: 0.8218 (m)
REVERT: A  439 ASP cc_start: 0.8375 (p0) cc_final: 0.8039 (t70)
REVERT: A  458 TYR cc_start: 0.9451 (t80) cc_final: 0.9239 (t80)
REVERT: A  537 LEU cc_start: 0.8965 (tp) cc_final: 0.8509 (tp)
REVERT: B  383 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7222 (mtm)
REVERT: C   24 LEU cc_start: 0.9285 (pp) cc_final: 0.9036 (mm)
REVERT: C   75 MET cc_start: 0.8580 (pmm) cc_final: 0.8345 (pmm)
REVERT: C  119 GLU cc_start: 0.8845 (mp0) cc_final: 0.8295 (mt-10)
  outliers start: 18
  outliers final: 13
  residues processed: 141
  average time/residue: 0.0728
  time to fit residues: 16.2326
Evaluate side-chains
  133 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   73 TRP
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue   10 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 65 optimal weight:   20.0000
   chunk 63 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0370
   chunk 91 optimal weight:    7.9990
   chunk 36 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.6862

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
B 338 GLN
C 131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.059002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.048643 restraints weight = 50517.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.050045 restraints weight = 24582.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.050861 restraints weight = 14719.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.051585 restraints weight = 10547.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.052011 restraints weight = 7715.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.4547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10986  Z= 0.119
  Angle     :  0.636   9.327  14954  Z= 0.310
  Chirality :  0.041   0.212   1803
  Planarity :  0.003   0.051   1898
  Dihedral  :  4.478  29.118   1524
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.03 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.16 (0.23), residues: 1436
  helix:  0.85 (0.18), residues: 848
  sheet: -0.84 (0.49), residues: 106
  loop : -1.61 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 213 
 TYR   0.027   0.002   TYR B 641 
 PHE   0.030   0.001   PHE C  13 
 TRP   0.037   0.001   TRP A 176 
 HIS   0.004   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10986)
  covalent geometry    : angle       0.63646 (14954)
  hydrogen bonds       : bond        0.03025 (  523)
  hydrogen bonds       : angle       4.25473 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.9302 (tt) cc_final: 0.9086 (tp)
REVERT: A  100 ASP cc_start: 0.8936 (p0) cc_final: 0.8191 (p0)
REVERT: A  256 MET cc_start: 0.8982 (mtp) cc_final: 0.8753 (mtt)
REVERT: A  380 LEU cc_start: 0.9321 (tp) cc_final: 0.8757 (tp)
REVERT: A  426 THR cc_start: 0.8549 (m) cc_final: 0.8185 (m)
REVERT: A  439 ASP cc_start: 0.8414 (p0) cc_final: 0.8074 (t70)
REVERT: A  537 LEU cc_start: 0.8895 (tp) cc_final: 0.8430 (tp)
REVERT: B  383 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7188 (mtm)
REVERT: C   24 LEU cc_start: 0.9297 (pp) cc_final: 0.9073 (mm)
REVERT: C   75 MET cc_start: 0.8606 (pmm) cc_final: 0.8364 (pmm)
REVERT: C  129 ASP cc_start: 0.8123 (t0) cc_final: 0.7831 (t70)
  outliers start: 17
  outliers final: 12
  residues processed: 144
  average time/residue: 0.0714
  time to fit residues: 16.3698
Evaluate side-chains
  136 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   73 TRP
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue   10 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 131 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0170
   chunk 62 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 133 optimal weight:    9.9990
   chunk 112 optimal weight:    4.9990
   chunk 65 optimal weight:   20.0000
   overall best weight:    1.0822

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** 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 = 0.3131 r_free = 0.3131 target = 0.059096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.048581 restraints weight = 50449.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.049958 restraints weight = 24965.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.050758 restraints weight = 15059.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.051457 restraints weight = 10880.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.051962 restraints weight = 8078.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10986  Z= 0.125
  Angle     :  0.664  11.586  14954  Z= 0.320
  Chirality :  0.041   0.156   1803
  Planarity :  0.003   0.050   1898
  Dihedral  :  4.454  30.165   1524
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 18.01 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.10 (0.22), residues: 1436
  helix:  0.91 (0.18), residues: 843
  sheet: -0.81 (0.49), residues: 106
  loop : -1.59 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 153 
 TYR   0.029   0.002   TYR B 641 
 PHE   0.026   0.001   PHE C  13 
 TRP   0.043   0.001   TRP A 176 
 HIS   0.003   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10986)
  covalent geometry    : angle       0.66412 (14954)
  hydrogen bonds       : bond        0.03035 (  523)
  hydrogen bonds       : angle       4.20405 ( 1515)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.8897 (p0) cc_final: 0.8231 (p0)
REVERT: A  255 GLN cc_start: 0.8221 (tt0) cc_final: 0.7888 (mt0)
REVERT: A  380 LEU cc_start: 0.9332 (tp) cc_final: 0.8773 (tp)
REVERT: A  439 ASP cc_start: 0.8421 (p0) cc_final: 0.8111 (t70)
REVERT: A  537 LEU cc_start: 0.8860 (tp) cc_final: 0.8298 (tp)
REVERT: B  383 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7183 (mtm)
REVERT: C   24 LEU cc_start: 0.9274 (pp) cc_final: 0.9064 (mm)
REVERT: C   75 MET cc_start: 0.8620 (pmm) cc_final: 0.8379 (pmm)
REVERT: C  119 GLU cc_start: 0.8853 (mp0) cc_final: 0.8236 (mt-10)
REVERT: C  129 ASP cc_start: 0.8133 (t0) cc_final: 0.7859 (t70)
  outliers start: 13
  outliers final: 11
  residues processed: 136
  average time/residue: 0.0642
  time to fit residues: 14.0265
Evaluate side-chains
  131 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   73 TRP
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain C residue   10 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0030
   chunk 6 optimal weight:    6.9990
   chunk 117 optimal weight:    0.0870
   overall best weight:    1.0174

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.059256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.048806 restraints weight = 50444.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.050236 restraints weight = 24902.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.051156 restraints weight = 14917.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.051788 restraints weight = 10255.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.052210 restraints weight = 7718.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.4750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10986  Z= 0.127
  Angle     :  0.668  11.067  14954  Z= 0.321
  Chirality :  0.041   0.225   1803
  Planarity :  0.003   0.050   1898
  Dihedral  :  4.442  30.965   1524
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 17.74 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.09 (0.22), residues: 1436
  helix:  0.88 (0.18), residues: 845
  sheet: -0.75 (0.49), residues: 106
  loop : -1.54 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 153 
 TYR   0.032   0.002   TYR A 458 
 PHE   0.062   0.002   PHE A 392 
 TRP   0.040   0.001   TRP A 176 
 HIS   0.003   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10986)
  covalent geometry    : angle       0.66768 (14954)
  hydrogen bonds       : bond        0.03043 (  523)
  hydrogen bonds       : angle       4.27582 ( 1515)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1487.87 seconds
wall clock time: 26 minutes 39.93 seconds (1599.93 seconds total)