Starting phenix.real_space_refine
on Thu Feb  5 10:09:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kox_62482/02_2026/9kox_62482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kox_62482/02_2026/9kox_62482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kox_62482/02_2026/9kox_62482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kox_62482/02_2026/9kox_62482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kox_62482/02_2026/9kox_62482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kox_62482/02_2026/9kox_62482.cif"
  }
  resolution = 4.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      85      5.16       5
     C   10307      2.51       5
     N    2761      2.21       5
     O    3100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16257
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 3229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3229
          Classifications: {'peptide': 409}
          Link IDs: {'PTRANS': 12, 'TRANS': 396}
    Chain: "B"
      Number of atoms: 5168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5168
          Classifications: {'peptide': 635}
          Link IDs: {'PTRANS': 15, 'TRANS': 619}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 5168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5168
          Classifications: {'peptide': 635}
          Link IDs: {'PTRANS': 15, 'TRANS': 619}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2638
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 21, 'TRANS': 321}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.58, per 1000 atoms: 0.22
  Number of scatterers: 16257
  At special positions: 0
  Unit cell: (113.061, 136.543, 140.891, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      85     16.00
     P       4     15.00
     O    3100      8.00
     N    2761      7.00
     C   10307      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: 1.66
  Conformation dependent library (CDL) restraints added in 828.5 milliseconds
  

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3808

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 16 sheets defined
      44.4% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'D' and resid 13 through 20
    Processing helix  chain 'D' and resid 87 through 95
      removed outlier: 3.673A  pdb=" N   ASP D  91 " --> pdb=" O   ILE D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 197
      removed outlier: 3.545A  pdb=" N   HIS D 196 " --> pdb=" O   GLU D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 206
    Processing helix  chain 'D' and resid 207 through 209
      No H-bonds generated for 'chain 'D' and resid 207 through 209'
    Processing helix  chain 'D' and resid 260 through 282
    Processing helix  chain 'D' and resid 286 through 299
      removed outlier: 3.832A  pdb=" N   GLN D 290 " --> pdb=" O   GLN D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 330
    Processing helix  chain 'D' and resid 333 through 347
    Processing helix  chain 'D' and resid 352 through 364
    Processing helix  chain 'D' and resid 366 through 381
    Processing helix  chain 'D' and resid 385 through 409
    Processing helix  chain 'D' and resid 411 through 420
      removed outlier: 3.656A  pdb=" N   LYS D 415 " --> pdb=" O   ASN D 411 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   PHE D 416 " --> pdb=" O   MET D 412 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA D 417 " --> pdb=" O   PHE D 413 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN D 419 " --> pdb=" O   LYS D 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 37
    Processing helix  chain 'B' and resid 40 through 42
      No H-bonds generated for 'chain 'B' and resid 40 through 42'
    Processing helix  chain 'B' and resid 43 through 66
      removed outlier: 4.208A  pdb=" N   GLU B  47 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU B  48 " --> pdb=" O   PHE B  44 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   ILE B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 74
      removed outlier: 3.724A  pdb=" N   SER B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 86
    Processing helix  chain 'B' and resid 99 through 107
    Processing helix  chain 'B' and resid 113 through 122
    Processing helix  chain 'B' and resid 137 through 142
    Processing helix  chain 'B' and resid 199 through 210
    Processing helix  chain 'B' and resid 305 through 318
      removed outlier: 4.000A  pdb=" N   TYR B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 430
      removed outlier: 3.769A  pdb=" N   ASP B 430 " --> pdb=" O   GLU B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 5.732A  pdb=" N   LYS B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ASN B 444 " --> pdb=" O   GLN B 440 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   SER B 453 " --> pdb=" O   ILE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 461
      removed outlier: 3.591A  pdb=" N   GLU B 461 " --> pdb=" O   LYS B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 481
    Processing helix  chain 'B' and resid 498 through 504
    Processing helix  chain 'B' and resid 505 through 515
    Processing helix  chain 'B' and resid 525 through 533
      removed outlier: 4.028A  pdb=" N   CYS B 529 " --> pdb=" O   ILE B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 539
      removed outlier: 3.532A  pdb=" N   GLY B 538 " --> pdb=" O   GLU B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 577
      removed outlier: 5.302A  pdb=" N   ASN B 570 " --> pdb=" O   THR B 566 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   LEU B 571 " --> pdb=" O   LYS B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 617
    Processing helix  chain 'B' and resid 622 through 627
      removed outlier: 3.549A  pdb=" N   TYR B 627 " --> pdb=" O   SER B 623 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 648
    Processing helix  chain 'B' and resid 656 through 673
    Processing helix  chain 'B' and resid 680 through 696
      removed outlier: 3.587A  pdb=" N   HIS B 684 " --> pdb=" O   ASP B 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 38
      removed outlier: 4.421A  pdb=" N   TYR A  38 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 44
      removed outlier: 3.702A  pdb=" N   ILE A  43 " --> pdb=" O   ASN A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 66
    Processing helix  chain 'A' and resid 66 through 74
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 99 through 108
      removed outlier: 3.921A  pdb=" N   ILE A 104 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 122
    Processing helix  chain 'A' and resid 137 through 144
    Processing helix  chain 'A' and resid 199 through 210
    Processing helix  chain 'A' and resid 307 through 317
    Processing helix  chain 'A' and resid 365 through 368
    Processing helix  chain 'A' and resid 374 through 378
    Processing helix  chain 'A' and resid 406 through 430
      removed outlier: 3.770A  pdb=" N   ASP A 430 " --> pdb=" O   GLU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 5.732A  pdb=" N   LYS A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ASN A 444 " --> pdb=" O   GLN A 440 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   SER A 453 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 460
    Processing helix  chain 'A' and resid 477 through 484
    Processing helix  chain 'A' and resid 485 through 488
    Processing helix  chain 'A' and resid 498 through 504
    Processing helix  chain 'A' and resid 505 through 514
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 3.911A  pdb=" N   CYS A 529 " --> pdb=" O   ILE A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 539
      removed outlier: 4.278A  pdb=" N   GLY A 538 " --> pdb=" O   GLU A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 577
      removed outlier: 5.415A  pdb=" N   ASN A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   LEU A 571 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 617
    Processing helix  chain 'A' and resid 622 through 627
      removed outlier: 3.934A  pdb=" N   TYR A 627 " --> pdb=" O   SER A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 651
      removed outlier: 4.641A  pdb=" N   LYS A 649 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLU A 651 " --> pdb=" O   ARG A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 673
    Processing helix  chain 'A' and resid 680 through 696
      removed outlier: 3.586A  pdb=" N   HIS A 684 " --> pdb=" O   ASP A 680 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 241
      removed outlier: 4.711A  pdb=" N   SER C 238 " --> pdb=" O   LEU C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 305 through 309
      removed outlier: 3.743A  pdb=" N   GLY C 309 " --> pdb=" O   GLU C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 332
      removed outlier: 3.645A  pdb=" N   CYS C 330 " --> pdb=" O   ARG C 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 356
      removed outlier: 3.549A  pdb=" N   GLY C 349 " --> pdb=" O   GLN C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 448
      removed outlier: 3.853A  pdb=" N   TYR C 444 " --> pdb=" O   GLY C 440 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU C 445 " --> pdb=" O   ALA C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 451 through 456
    Processing helix  chain 'C' and resid 466 through 470
    Processing helix  chain 'C' and resid 479 through 489
    Processing helix  chain 'C' and resid 499 through 512
    Processing helix  chain 'C' and resid 529 through 538
    Processing helix  chain 'C' and resid 539 through 542
    Processing helix  chain 'C' and resid 549 through 554
      removed outlier: 4.249A  pdb=" N   LYS C 553 " --> pdb=" O   CYS C 549 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   MET C 554 " --> pdb=" O   VAL C 550 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 549 through 554'
    Processing helix  chain 'C' and resid 555 through 560
    Processing helix  chain 'C' and resid 563 through 566
    Processing helix  chain 'C' and resid 567 through 580
      removed outlier: 4.322A  pdb=" N   ALA C 571 " --> pdb=" O   LEU C 567 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TRP C 577 " --> pdb=" O   LEU C 573 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG C 578 " --> pdb=" O   LEU C 574 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 24 through 25
    Processing sheet with id=AA2, first strand: chain 'D' and resid 150 through 152
      removed outlier: 3.619A  pdb=" N   ARG D 151 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   CYS D 215 " --> pdb=" O   VAL D 245 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   VAL D 245 " --> pdb=" O   CYS D 215 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   GLU D 169 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21
      removed outlier: 3.938A  pdb=" N   THR A 171 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 184 through 189
      removed outlier: 6.194A  pdb=" N   ILE B  78 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152
      removed outlier: 3.957A  pdb=" N   THR B 171 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 323 through 330
      removed outlier: 3.517A  pdb=" N   LEU B 340 " --> pdb=" O   VAL B 388 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   LYS B 362 " --> pdb=" O   VAL B 389 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 519 through 521
      removed outlier: 8.268A  pdb=" N   ILE B 519 " --> pdb=" O   HIS B 490 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TYR B 492 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   MET B 521 " --> pdb=" O   TYR B 492 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   ILE B 494 " --> pdb=" O   MET B 521 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   ILE B 491 " --> pdb=" O   VAL B 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 597 through 599
    Processing sheet with id=AA9, first strand: chain 'A' and resid 78 through 80
    Processing sheet with id=AB1, first strand: chain 'A' and resid 219 through 222
    Processing sheet with id=AB2, first strand: chain 'A' and resid 323 through 330
      removed outlier: 3.518A  pdb=" N   LEU A 340 " --> pdb=" O   VAL A 388 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ARG A 386 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AB4, first strand: chain 'A' and resid 519 through 521
      removed outlier: 8.805A  pdb=" N   ILE A 519 " --> pdb=" O   HIS A 490 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   TYR A 492 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   MET A 521 " --> pdb=" O   TYR A 492 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   ILE A 494 " --> pdb=" O   MET A 521 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE A 491 " --> pdb=" O   VAL A 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 597 through 601
      removed outlier: 3.771A  pdb=" N   HIS A 633 " --> pdb=" O   VAL A 600 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 171
    Processing sheet with id=AB7, first strand: chain 'C' and resid 323 through 324
      removed outlier: 3.887A  pdb=" N   CYS C 323 " --> pdb=" O   VAL C 370 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1752 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: 2.51

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2813
        1.31 -     1.44: 4066
        1.44 -     1.57: 9518
        1.57 -     1.69: 6
        1.69 -     1.82: 137
  Bond restraints: 16540
  Sorted by residual:
  bond pdb=" C   MET A 575 "
       pdb=" O   MET A 575 "
    ideal  model  delta    sigma   weight residual
    1.237  1.192  0.045 1.16e-02 7.43e+03 1.48e+01
  bond pdb=" CA  LEU A  76 "
       pdb=" C   LEU A  76 "
    ideal  model  delta    sigma   weight residual
    1.523  1.476  0.047 1.24e-02 6.50e+03 1.44e+01
  bond pdb=" C   THR B  99 "
       pdb=" O   THR B  99 "
    ideal  model  delta    sigma   weight residual
    1.234  1.183  0.051 1.36e-02 5.41e+03 1.42e+01
  bond pdb=" CA  ARG B  46 "
       pdb=" C   ARG B  46 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.050 1.34e-02 5.57e+03 1.39e+01
  bond pdb=" C   ALA A 347 "
       pdb=" N   PRO A 348 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 8.70e-03 1.32e+04 1.32e+01
  ... (remaining 16535 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 20768
        2.24 -     4.48: 1263
        4.48 -     6.71: 185
        6.71 -     8.95: 29
        8.95 -    11.19: 10
  Bond angle restraints: 22255
  Sorted by residual:
  angle pdb=" N   CYS D 107 "
        pdb=" CA  CYS D 107 "
        pdb=" C   CYS D 107 "
      ideal   model   delta    sigma   weight residual
     110.10  117.50   -7.40 1.49e+00 4.50e-01 2.46e+01
  angle pdb=" C   ASN A 300 "
        pdb=" N   PRO A 301 "
        pdb=" CA  PRO A 301 "
      ideal   model   delta    sigma   weight residual
     120.03  115.12    4.91 9.90e-01 1.02e+00 2.46e+01
  angle pdb=" C   SER D 115 "
        pdb=" CA  SER D 115 "
        pdb=" CB  SER D 115 "
      ideal   model   delta    sigma   weight residual
     116.63  110.91    5.72 1.16e+00 7.43e-01 2.43e+01
  angle pdb=" N   ASN A 590 "
        pdb=" CA  ASN A 590 "
        pdb=" C   ASN A 590 "
      ideal   model   delta    sigma   weight residual
     112.92  106.88    6.04 1.23e+00 6.61e-01 2.41e+01
  angle pdb=" N   THR A 115 "
        pdb=" CA  THR A 115 "
        pdb=" C   THR A 115 "
      ideal   model   delta    sigma   weight residual
     111.03  105.60    5.43 1.11e+00 8.12e-01 2.40e+01
  ... (remaining 22250 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.90: 8594
       20.90 -    41.80: 1059
       41.80 -    62.69: 453
       62.69 -    83.59: 55
       83.59 -   104.49: 10
  Dihedral angle restraints: 10171
    sinusoidal: 4272
      harmonic: 5899
  Sorted by residual:
  dihedral pdb=" O2A ADP B 801 "
           pdb=" O3A ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" PB  ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   44.49 -104.49     1      2.00e+01 2.50e-03 3.00e+01
  dihedral pdb=" O2A ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" PB  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   44.45 -104.45     1      2.00e+01 2.50e-03 3.00e+01
  dihedral pdb=" CA  ALA C 255 "
           pdb=" C   ALA C 255 "
           pdb=" N   VAL C 256 "
           pdb=" CA  VAL C 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.38   24.62     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 10168 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1893
       0.077 -    0.154: 437
       0.154 -    0.231: 110
       0.231 -    0.308: 17
       0.308 -    0.385: 5
  Chirality restraints: 2462
  Sorted by residual:
  chirality pdb=" CA  ASN A 373 "
            pdb=" N   ASN A 373 "
            pdb=" C   ASN A 373 "
            pdb=" CB  ASN A 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CA  THR A 176 "
            pdb=" N   THR A 176 "
            pdb=" C   THR A 176 "
            pdb=" CB  THR A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  ASP A 661 "
            pdb=" N   ASP A 661 "
            pdb=" C   ASP A 661 "
            pdb=" CB  ASP A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.68e+00
  ... (remaining 2459 not shown)

  Planarity restraints: 2841
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 130 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.79e+00
        pdb=" C   PHE D 130 "    0.054 2.00e-02 2.50e+03
        pdb=" O   PHE D 130 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU D 131 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 451 "    0.050 5.00e-02 4.00e+02   7.82e-02 9.78e+00
        pdb=" N   PRO C 452 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO C 452 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 452 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D 411 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   ASN D 411 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ASN D 411 "    0.018 2.00e-02 2.50e+03
        pdb=" N   MET D 412 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2838 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 1528
        2.71 -     3.26: 18929
        3.26 -     3.81: 29300
        3.81 -     4.35: 35957
        4.35 -     4.90: 52611
  Nonbonded interactions: 138325
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 308 "
            pdb=" OE1 GLU B 308 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" NH2 ARG B 512 "
            pdb=" OH  TYR B 520 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ASN C 235 "
            pdb=" OG  SER C 238 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   ALA B 126 "
            pdb=" OD1 ASP B 127 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   GLU B 336 "
            pdb=" OG  SER B 391 "
     model   vdw
     2.215 3.040
  ... (remaining 138320 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.990
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:1.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
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   0.105  16540  Z= 0.521
  Angle     :  1.193  11.189  22255  Z= 0.758
  Chirality :  0.073   0.385   2462
  Planarity :  0.006   0.078   2841
  Dihedral  : 21.328 104.491   6363
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 36.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers : 19.33 %
    Allowed  : 15.45 %
    Favored  : 65.22 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.75 (0.16), residues: 2006
  helix: -2.07 (0.17), residues: 760
  sheet: -3.02 (0.34), residues: 171
  loop : -2.76 (0.16), residues: 1075

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 312 
 TYR   0.024   0.002   TYR A 216 
 PHE   0.024   0.002   PHE C 453 
 TRP   0.015   0.003   TRP B 162 
 HIS   0.011   0.002   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00796 (16540)
  covalent geometry    : angle       1.19315 (22255)
  hydrogen bonds       : bond        0.21566 (  625)
  hydrogen bonds       : angle       8.44935 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  886 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 343
    poor density    : 543
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   24 ASP cc_start: 0.8262 (p0) cc_final: 0.7304 (p0)
REVERT: D   61 LEU cc_start: 0.9154 (mt) cc_final: 0.8900 (mt)
REVERT: D  107 CYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5468 (p)
REVERT: D  131 GLU cc_start: 0.8713 (mp0) cc_final: 0.8397 (mt-10)
REVERT: D  163 ASN cc_start: 0.8193 (m-40) cc_final: 0.7978 (m-40)
REVERT: D  300 MET cc_start: 0.9258 (tpp) cc_final: 0.8915 (tpp)
REVERT: D  301 GLU cc_start: 0.9257 (pt0) cc_final: 0.8898 (mp0)
REVERT: D  351 GLU cc_start: 0.8094 (mp0) cc_final: 0.7881 (pm20)
REVERT: D  364 MET cc_start: 0.8434 (mtm) cc_final: 0.8047 (tpt)
REVERT: D  374 PHE cc_start: 0.8083 (m-80) cc_final: 0.6076 (m-80)
REVERT: D  404 ARG cc_start: 0.7192 (ttp-170) cc_final: 0.6874 (ttp-170)
REVERT: B   39 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7659 (t)
REVERT: B   45 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9011 (mt)
REVERT: B   46 ARG cc_start: 0.9616 (tmm-80) cc_final: 0.9312 (mtm110)
REVERT: B   62 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8965 (tm-30)
REVERT: B   78 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: B  106 ASN cc_start: 0.9354 (p0) cc_final: 0.9058 (p0)
REVERT: B  118 PHE cc_start: 0.9530 (t80) cc_final: 0.9262 (t80)
REVERT: B  133 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7991 (pp30)
REVERT: B  146 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7327 (mp0)
REVERT: B  374 CYS cc_start: 0.6886 (OUTLIER) cc_final: 0.5866 (t)
REVERT: B  376 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8243 (mp0)
REVERT: B  426 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8782 (mm-30)
REVERT: B  498 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7962 (p)
REVERT: B  500 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8560 (p0)
REVERT: B  509 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9079 (mm-30)
REVERT: B  521 MET cc_start: 0.8339 (mmm) cc_final: 0.7975 (mmt)
REVERT: B  522 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8534 (mt)
REVERT: B  523 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8108 (mt-10)
REVERT: B  536 PHE cc_start: 0.8434 (t80) cc_final: 0.8108 (t80)
REVERT: B  537 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8711 (tm-30)
REVERT: B  549 LEU cc_start: 0.8878 (tp) cc_final: 0.8497 (tp)
REVERT: B  585 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9094 (tptp)
REVERT: B  587 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8259 (m)
REVERT: B  595 SER cc_start: 0.9198 (t) cc_final: 0.8872 (m)
REVERT: B  628 MET cc_start: 0.5997 (mmm) cc_final: 0.5714 (tpp)
REVERT: B  651 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8945 (pm20)
REVERT: B  684 HIS cc_start: 0.9094 (t-170) cc_final: 0.8557 (t70)
REVERT: A   51 ASN cc_start: 0.9295 (m-40) cc_final: 0.8868 (t0)
REVERT: A  100 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8855 (ttpt)
REVERT: A  113 SER cc_start: 0.4256 (OUTLIER) cc_final: 0.3910 (t)
REVERT: A  119 MET cc_start: 0.9013 (tmm) cc_final: 0.8742 (tmm)
REVERT: A  128 ILE cc_start: 0.8432 (mm) cc_final: 0.7315 (mm)
REVERT: A  188 LEU cc_start: 0.8266 (tt) cc_final: 0.8033 (mp)
REVERT: A  200 GLU cc_start: 0.9221 (pm20) cc_final: 0.8953 (pm20)
REVERT: A  204 LYS cc_start: 0.8883 (mptt) cc_final: 0.8507 (tttt)
REVERT: A  279 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5742 (tttt)
REVERT: A  299 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9076 (mpt180)
REVERT: A  305 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.6880 (t)
REVERT: A  367 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8070 (mtp-110)
REVERT: A  439 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8571 (tm-30)
REVERT: A  455 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8359 (p0)
REVERT: A  463 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7509 (mm)
REVERT: A  464 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8586 (mmt180)
REVERT: A  486 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8258 (tp30)
REVERT: A  487 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8761 (p0)
REVERT: A  493 TYR cc_start: 0.9351 (p90) cc_final: 0.9110 (p90)
REVERT: A  499 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8493 (tptp)
REVERT: A  555 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9085 (pm20)
REVERT: A  620 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6155 (tpt90)
REVERT: A  633 HIS cc_start: 0.8553 (p90) cc_final: 0.8227 (p-80)
REVERT: A  655 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8162 (p0)
REVERT: C  332 ASN cc_start: 0.8291 (m110) cc_final: 0.7810 (t0)
REVERT: C  342 MET cc_start: 0.8023 (mmt) cc_final: 0.7758 (mmm)
REVERT: C  382 ILE cc_start: -0.2904 (OUTLIER) cc_final: -0.3105 (mm)
REVERT: C  501 ARG cc_start: 0.8721 (tpt90) cc_final: 0.8491 (tpt90)
REVERT: C  512 TRP cc_start: 0.8582 (m-90) cc_final: 0.8176 (m-90)
  outliers start: 343
  outliers final: 98
  residues processed: 760
  average time/residue: 0.1440
  time to fit residues: 152.0995
Evaluate side-chains
  520 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 128
    poor density    : 392
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
D  21 GLN
D  74 ASN
D 210 GLN
D 286 GLN
D 365 ASN
D 383 GLN
D 384 ASN
B  23 GLN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 HIS
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
B 504 ASN
B 561 GLN
A  23 GLN
A 105 ASN
** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 GLN
A 210 HIS
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 ASN
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 GLN
C 235 ASN
** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN
** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.160649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.124867 restraints weight = 49482.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.128673 restraints weight = 33467.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.131307 restraints weight = 24729.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.133214 restraints weight = 19665.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.134533 restraints weight = 16488.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  16540  Z= 0.209
  Angle     :  0.819  11.863  22255  Z= 0.428
  Chirality :  0.050   0.205   2462
  Planarity :  0.006   0.047   2841
  Dihedral  :  7.532 120.133   2207
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 26.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.78 %
    Favored  : 91.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.17), residues: 2006
  helix: -1.42 (0.16), residues: 796
  sheet: -2.96 (0.32), residues: 206
  loop : -2.26 (0.19), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 687 
 TYR   0.033   0.002   TYR D 278 
 PHE   0.033   0.003   PHE D 320 
 TRP   0.036   0.003   TRP B 162 
 HIS   0.007   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (16540)
  covalent geometry    : angle       0.81950 (22255)
  hydrogen bonds       : bond        0.05464 (  625)
  hydrogen bonds       : angle       6.60165 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  501 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 493
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8259 (mp0) cc_final: 0.7626 (mp0)
REVERT: D   35 LYS cc_start: 0.9343 (pptt) cc_final: 0.8795 (ttpt)
REVERT: D   61 LEU cc_start: 0.9303 (mt) cc_final: 0.9041 (mt)
REVERT: D  105 LEU cc_start: 0.8645 (mt) cc_final: 0.8227 (mt)
REVERT: D  130 PHE cc_start: 0.7141 (p90) cc_final: 0.6290 (p90)
REVERT: D  150 ARG cc_start: 0.8201 (tpt-90) cc_final: 0.7983 (tpt170)
REVERT: D  163 ASN cc_start: 0.8227 (m-40) cc_final: 0.7427 (p0)
REVERT: D  297 TRP cc_start: 0.8199 (m-10) cc_final: 0.7834 (m-10)
REVERT: D  301 GLU cc_start: 0.9287 (pt0) cc_final: 0.9014 (pm20)
REVERT: D  402 ASN cc_start: 0.7851 (m110) cc_final: 0.7352 (m-40)
REVERT: D  406 ARG cc_start: 0.7983 (mpt90) cc_final: 0.7567 (mtt-85)
REVERT: D  412 MET cc_start: 0.6119 (pmm) cc_final: 0.5857 (pmm)
REVERT: B   39 SER cc_start: 0.8107 (p) cc_final: 0.7848 (t)
REVERT: B   62 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8671 (tm-30)
REVERT: B  107 LEU cc_start: 0.8649 (tt) cc_final: 0.8265 (tt)
REVERT: B  116 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9094 (tttp)
REVERT: B  118 PHE cc_start: 0.9466 (t80) cc_final: 0.9186 (t80)
REVERT: B  138 PHE cc_start: 0.8367 (t80) cc_final: 0.8042 (t80)
REVERT: B  162 TRP cc_start: 0.8545 (t-100) cc_final: 0.8329 (t60)
REVERT: B  218 ILE cc_start: 0.9050 (pt) cc_final: 0.8648 (tp)
REVERT: B  289 GLU cc_start: 0.8038 (pp20) cc_final: 0.7827 (pp20)
REVERT: B  291 ASN cc_start: 0.7540 (p0) cc_final: 0.7278 (p0)
REVERT: B  345 ARG cc_start: 0.6313 (ttm-80) cc_final: 0.5514 (ttm-80)
REVERT: B  364 TYR cc_start: 0.8681 (m-10) cc_final: 0.8473 (m-10)
REVERT: B  401 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8996 (mt-10)
REVERT: B  435 LYS cc_start: 0.9075 (pttp) cc_final: 0.8835 (pptt)
REVERT: B  446 LYS cc_start: 0.9503 (mmpt) cc_final: 0.9259 (mmmt)
REVERT: B  480 TYR cc_start: 0.8792 (t80) cc_final: 0.8376 (t80)
REVERT: B  484 MET cc_start: 0.3152 (mmm) cc_final: 0.2891 (mmm)
REVERT: B  490 HIS cc_start: 0.7649 (m90) cc_final: 0.7409 (m90)
REVERT: B  510 ARG cc_start: 0.8225 (tpt-90) cc_final: 0.6930 (tpt-90)
REVERT: B  518 VAL cc_start: 0.9573 (p) cc_final: 0.9369 (p)
REVERT: B  519 ILE cc_start: 0.9387 (tt) cc_final: 0.9103 (tt)
REVERT: B  523 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8852 (mp0)
REVERT: B  536 PHE cc_start: 0.8505 (t80) cc_final: 0.8239 (t80)
REVERT: B  537 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: B  568 PHE cc_start: 0.9001 (m-10) cc_final: 0.8768 (m-10)
REVERT: B  598 CYS cc_start: 0.8728 (t) cc_final: 0.8250 (t)
REVERT: A   30 MET cc_start: 0.9087 (ttp) cc_final: 0.8799 (tmm)
REVERT: A   51 ASN cc_start: 0.9192 (m-40) cc_final: 0.8826 (t0)
REVERT: A   62 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9028 (tp30)
REVERT: A   83 ASN cc_start: 0.9054 (m-40) cc_final: 0.8604 (m-40)
REVERT: A   84 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9134 (mmmt)
REVERT: A  119 MET cc_start: 0.8835 (tmm) cc_final: 0.8547 (tmm)
REVERT: A  128 ILE cc_start: 0.8843 (mm) cc_final: 0.8041 (mm)
REVERT: A  170 PHE cc_start: 0.9064 (p90) cc_final: 0.8703 (p90)
REVERT: A  180 MET cc_start: 0.9027 (mtm) cc_final: 0.8717 (mtm)
REVERT: A  188 LEU cc_start: 0.8488 (tt) cc_final: 0.8033 (mp)
REVERT: A  196 GLU cc_start: 0.8058 (mp0) cc_final: 0.7339 (mp0)
REVERT: A  200 GLU cc_start: 0.9247 (pm20) cc_final: 0.8683 (pm20)
REVERT: A  213 PHE cc_start: 0.7519 (m-80) cc_final: 0.7031 (m-10)
REVERT: A  308 GLU cc_start: 0.8146 (tp30) cc_final: 0.7570 (tp30)
REVERT: A  312 PHE cc_start: 0.9087 (t80) cc_final: 0.8883 (t80)
REVERT: A  314 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8136 (mmmt)
REVERT: A  357 LYS cc_start: 0.2682 (tmtt) cc_final: 0.2324 (tptt)
REVERT: A  439 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8268 (tm-30)
REVERT: A  514 HIS cc_start: 0.8324 (m-70) cc_final: 0.7831 (m90)
REVERT: A  523 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8279 (mt-10)
REVERT: A  534 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8290 (mmmm)
REVERT: A  597 CYS cc_start: 0.9072 (m) cc_final: 0.8431 (t)
REVERT: A  615 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8129 (mmtt)
REVERT: A  620 ARG cc_start: 0.7339 (tmt-80) cc_final: 0.7081 (tpt90)
REVERT: A  633 HIS cc_start: 0.8518 (p90) cc_final: 0.7999 (p90)
REVERT: A  636 ILE cc_start: 0.9345 (pt) cc_final: 0.8668 (pt)
REVERT: A  662 LEU cc_start: 0.9366 (mm) cc_final: 0.9161 (mm)
REVERT: C  324 THR cc_start: 0.8930 (t) cc_final: 0.8367 (t)
REVERT: C  332 ASN cc_start: 0.8384 (m-40) cc_final: 0.8076 (t0)
REVERT: C  512 TRP cc_start: 0.8162 (m-90) cc_final: 0.7859 (m-90)
  outliers start: 8
  outliers final: 4
  residues processed: 499
  average time/residue: 0.1250
  time to fit residues: 90.2420
Evaluate side-chains
  398 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 394
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 191 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 181 optimal weight:    5.9990
   chunk 134 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   chunk 190 optimal weight:    0.7980
   chunk 165 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 114 optimal weight:    9.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
D 365 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 561 GLN
A 105 ASN
** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 HIS
A 318 ASN
A 323 HIS
A 328 HIS
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 356 GLN
** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.160396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.123429 restraints weight = 48985.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.127182 restraints weight = 33238.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.129925 restraints weight = 24807.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.131662 restraints weight = 19786.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.133158 restraints weight = 16732.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.4928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  16540  Z= 0.174
  Angle     :  0.743  11.700  22255  Z= 0.383
  Chirality :  0.047   0.199   2462
  Planarity :  0.005   0.057   2841
  Dihedral  :  7.243 120.296   2207
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 22.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.03 %
    Favored  : 93.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.17), residues: 2006
  helix: -0.95 (0.17), residues: 801
  sheet: -2.67 (0.34), residues: 200
  loop : -2.15 (0.19), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 687 
 TYR   0.031   0.002   TYR A 528 
 PHE   0.020   0.002   PHE D 374 
 TRP   0.028   0.002   TRP B 162 
 HIS   0.006   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (16540)
  covalent geometry    : angle       0.74262 (22255)
  hydrogen bonds       : bond        0.04745 (  625)
  hydrogen bonds       : angle       6.13597 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  464 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 462
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8152 (mp0) cc_final: 0.7209 (mp0)
REVERT: D   35 LYS cc_start: 0.9340 (pptt) cc_final: 0.8753 (tmmt)
REVERT: D   61 LEU cc_start: 0.9316 (mt) cc_final: 0.9089 (mt)
REVERT: D  105 LEU cc_start: 0.8430 (mt) cc_final: 0.7972 (mt)
REVERT: D  130 PHE cc_start: 0.6678 (p90) cc_final: 0.5693 (p90)
REVERT: D  163 ASN cc_start: 0.8291 (m-40) cc_final: 0.7528 (p0)
REVERT: D  241 LEU cc_start: 0.9440 (mt) cc_final: 0.9227 (mt)
REVERT: D  297 TRP cc_start: 0.8060 (m-10) cc_final: 0.7719 (m-10)
REVERT: D  300 MET cc_start: 0.9210 (tpp) cc_final: 0.8841 (tpp)
REVERT: D  301 GLU cc_start: 0.9311 (pt0) cc_final: 0.8946 (mp0)
REVERT: D  409 TYR cc_start: 0.8711 (m-80) cc_final: 0.8281 (m-80)
REVERT: D  412 MET cc_start: 0.6583 (pmm) cc_final: 0.6014 (pmm)
REVERT: B   39 SER cc_start: 0.8218 (p) cc_final: 0.7835 (t)
REVERT: B   62 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8752 (tm-30)
REVERT: B  118 PHE cc_start: 0.9464 (t80) cc_final: 0.9217 (t80)
REVERT: B  218 ILE cc_start: 0.9121 (pt) cc_final: 0.8777 (tp)
REVERT: B  345 ARG cc_start: 0.6361 (ttm-80) cc_final: 0.5470 (ttm-80)
REVERT: B  364 TYR cc_start: 0.8632 (m-10) cc_final: 0.8411 (m-10)
REVERT: B  371 MET cc_start: 0.7730 (tmm) cc_final: 0.7472 (tmm)
REVERT: B  394 LEU cc_start: 0.8866 (mm) cc_final: 0.8658 (mm)
REVERT: B  401 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8828 (mt-10)
REVERT: B  420 CYS cc_start: 0.8796 (p) cc_final: 0.8549 (p)
REVERT: B  484 MET cc_start: 0.3169 (mmm) cc_final: 0.2804 (mmm)
REVERT: B  510 ARG cc_start: 0.8064 (tpt-90) cc_final: 0.6837 (tpt-90)
REVERT: B  519 ILE cc_start: 0.9388 (tt) cc_final: 0.9154 (tp)
REVERT: B  523 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8886 (mp0)
REVERT: B  526 ASP cc_start: 0.8517 (t0) cc_final: 0.8018 (t0)
REVERT: B  537 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: B  568 PHE cc_start: 0.8899 (m-10) cc_final: 0.8656 (m-10)
REVERT: B  598 CYS cc_start: 0.8746 (t) cc_final: 0.8358 (t)
REVERT: B  647 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7500 (ttp80)
REVERT: A   30 MET cc_start: 0.9050 (ttp) cc_final: 0.8580 (ppp)
REVERT: A   62 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9072 (tp30)
REVERT: A   83 ASN cc_start: 0.9057 (m-40) cc_final: 0.8616 (m-40)
REVERT: A  116 LYS cc_start: 0.9452 (pttm) cc_final: 0.9117 (pttp)
REVERT: A  128 ILE cc_start: 0.8725 (mm) cc_final: 0.7969 (mm)
REVERT: A  180 MET cc_start: 0.9168 (mtm) cc_final: 0.8552 (mtt)
REVERT: A  188 LEU cc_start: 0.8494 (tt) cc_final: 0.8009 (mp)
REVERT: A  213 PHE cc_start: 0.8337 (m-80) cc_final: 0.7151 (m-10)
REVERT: A  308 GLU cc_start: 0.8107 (tp30) cc_final: 0.7504 (tp30)
REVERT: A  314 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8239 (mmmt)
REVERT: A  394 LEU cc_start: 0.8879 (mt) cc_final: 0.8531 (mt)
REVERT: A  458 LYS cc_start: 0.9133 (mppt) cc_final: 0.8909 (mppt)
REVERT: A  521 MET cc_start: 0.8338 (mmp) cc_final: 0.7794 (mmp)
REVERT: A  523 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8608 (mt-10)
REVERT: A  534 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8217 (mmmm)
REVERT: A  597 CYS cc_start: 0.9037 (m) cc_final: 0.8548 (t)
REVERT: A  611 GLU cc_start: 0.9518 (tt0) cc_final: 0.9286 (tt0)
REVERT: A  628 MET cc_start: 0.4663 (mmm) cc_final: 0.3987 (mmm)
REVERT: A  633 HIS cc_start: 0.8141 (p90) cc_final: 0.7884 (p90)
REVERT: A  636 ILE cc_start: 0.9474 (pt) cc_final: 0.9249 (pt)
REVERT: A  679 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8936 (tm-30)
REVERT: C  318 MET cc_start: 0.6291 (tmm) cc_final: 0.6089 (tpp)
REVERT: C  332 ASN cc_start: 0.8329 (m-40) cc_final: 0.8098 (t0)
REVERT: C  342 MET cc_start: 0.7926 (mmm) cc_final: 0.7531 (mmm)
REVERT: C  351 ASP cc_start: 0.8427 (t0) cc_final: 0.8192 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 462
  average time/residue: 0.1238
  time to fit residues: 83.8068
Evaluate side-chains
  370 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 369
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 88 optimal weight:    9.9990
   chunk 139 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0070
   chunk 51 optimal weight:   20.0000
   chunk 83 optimal weight:    0.1980
   chunk 16 optimal weight:    9.9990
   chunk 176 optimal weight:    0.3980
   chunk 196 optimal weight:   20.0000
   chunk 113 optimal weight:    9.9990
   overall best weight:    2.9202

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

Flipped N/Q/H residues before XYZ refinement:
D 402 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 HIS
A  83 ASN
** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 HIS
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.156763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.120065 restraints weight = 49476.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.123560 restraints weight = 34195.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.125900 restraints weight = 25569.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.127806 restraints weight = 20697.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.129020 restraints weight = 17555.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  16540  Z= 0.190
  Angle     :  0.744  12.236  22255  Z= 0.389
  Chirality :  0.047   0.205   2462
  Planarity :  0.005   0.045   2841
  Dihedral  :  7.239 123.604   2207
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 24.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  5.41 %
    Favored  : 94.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.17), residues: 2006
  helix: -0.87 (0.17), residues: 813
  sheet: -2.36 (0.35), residues: 192
  loop : -2.18 (0.19), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 687 
 TYR   0.036   0.002   TYR D 278 
 PHE   0.019   0.002   PHE D  67 
 TRP   0.049   0.003   TRP B 162 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (16540)
  covalent geometry    : angle       0.74432 (22255)
  hydrogen bonds       : bond        0.04598 (  625)
  hydrogen bonds       : angle       6.08727 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  450 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 447
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8210 (mp0) cc_final: 0.7318 (mp0)
REVERT: D   35 LYS cc_start: 0.9290 (pptt) cc_final: 0.8726 (tmmt)
REVERT: D  105 LEU cc_start: 0.8511 (mt) cc_final: 0.8186 (mt)
REVERT: D  163 ASN cc_start: 0.8328 (m-40) cc_final: 0.7557 (p0)
REVERT: D  297 TRP cc_start: 0.8138 (m-10) cc_final: 0.7836 (m-10)
REVERT: D  301 GLU cc_start: 0.9323 (pt0) cc_final: 0.9025 (pp20)
REVERT: D  409 TYR cc_start: 0.8730 (m-80) cc_final: 0.8328 (m-80)
REVERT: B   28 GLN cc_start: 0.9121 (pm20) cc_final: 0.8141 (pp30)
REVERT: B   30 MET cc_start: 0.9090 (ttt) cc_final: 0.8717 (tmm)
REVERT: B   39 SER cc_start: 0.8339 (p) cc_final: 0.8003 (t)
REVERT: B   62 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8764 (tm-30)
REVERT: B  118 PHE cc_start: 0.9492 (t80) cc_final: 0.9247 (t80)
REVERT: B  138 PHE cc_start: 0.8503 (t80) cc_final: 0.8123 (t80)
REVERT: B  203 ILE cc_start: 0.9416 (mt) cc_final: 0.9147 (mt)
REVERT: B  213 PHE cc_start: 0.8397 (m-80) cc_final: 0.6933 (m-10)
REVERT: B  302 ASP cc_start: 0.8798 (m-30) cc_final: 0.8399 (t0)
REVERT: B  345 ARG cc_start: 0.6305 (ttm-80) cc_final: 0.5445 (ttm-80)
REVERT: B  364 TYR cc_start: 0.8722 (m-10) cc_final: 0.8366 (m-10)
REVERT: B  394 LEU cc_start: 0.8854 (mm) cc_final: 0.8582 (mm)
REVERT: B  401 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8719 (mp0)
REVERT: B  416 LEU cc_start: 0.9471 (mt) cc_final: 0.9218 (tp)
REVERT: B  419 LYS cc_start: 0.8105 (mmtm) cc_final: 0.7849 (mmtm)
REVERT: B  420 CYS cc_start: 0.8615 (p) cc_final: 0.8402 (p)
REVERT: B  484 MET cc_start: 0.3286 (mmm) cc_final: 0.2774 (mmm)
REVERT: B  510 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.6766 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: B  568 PHE cc_start: 0.8991 (m-10) cc_final: 0.8790 (m-10)
REVERT: B  598 CYS cc_start: 0.8973 (t) cc_final: 0.8661 (t)
REVERT: B  620 ARG cc_start: 0.8510 (tmt-80) cc_final: 0.8127 (tpt90)
REVERT: B  621 ASP cc_start: 0.8143 (m-30) cc_final: 0.7698 (m-30)
REVERT: B  622 ASN cc_start: 0.7344 (m110) cc_final: 0.6963 (m110)
REVERT: B  647 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7691 (ttp80)
REVERT: B  678 LEU cc_start: 0.8999 (tp) cc_final: 0.8707 (tp)
REVERT: A   30 MET cc_start: 0.9063 (ttp) cc_final: 0.8516 (ppp)
REVERT: A   62 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9088 (tp30)
REVERT: A   83 ASN cc_start: 0.9043 (m110) cc_final: 0.8674 (m110)
REVERT: A  119 MET cc_start: 0.8962 (tmm) cc_final: 0.8713 (tmm)
REVERT: A  134 PHE cc_start: 0.8784 (m-10) cc_final: 0.8526 (m-80)
REVERT: A  180 MET cc_start: 0.9185 (mtm) cc_final: 0.8617 (mtm)
REVERT: A  188 LEU cc_start: 0.8480 (tt) cc_final: 0.7985 (mp)
REVERT: A  194 GLN cc_start: 0.8582 (mp10) cc_final: 0.8271 (mp10)
REVERT: A  213 PHE cc_start: 0.7986 (m-80) cc_final: 0.7267 (m-10)
REVERT: A  306 ASN cc_start: 0.8696 (m-40) cc_final: 0.8379 (p0)
REVERT: A  314 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8382 (mmmt)
REVERT: A  361 ILE cc_start: 0.8592 (mm) cc_final: 0.8385 (mm)
REVERT: A  394 LEU cc_start: 0.8932 (mt) cc_final: 0.8528 (mt)
REVERT: A  480 TYR cc_start: 0.8124 (t80) cc_final: 0.7914 (t80)
REVERT: A  521 MET cc_start: 0.8501 (mmp) cc_final: 0.8191 (mmp)
REVERT: A  523 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8702 (mt-10)
REVERT: A  534 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8459 (mmmm)
REVERT: A  597 CYS cc_start: 0.9125 (m) cc_final: 0.8655 (t)
REVERT: A  604 TYR cc_start: 0.6860 (t80) cc_final: 0.6276 (t80)
REVERT: A  611 GLU cc_start: 0.9525 (tt0) cc_final: 0.9260 (tt0)
REVERT: A  620 ARG cc_start: 0.7667 (tpt90) cc_final: 0.6810 (tpt90)
REVERT: A  633 HIS cc_start: 0.8110 (p90) cc_final: 0.7727 (p90)
REVERT: A  636 ILE cc_start: 0.9515 (pt) cc_final: 0.9282 (pt)
REVERT: A  679 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8967 (tm-30)
REVERT: C  332 ASN cc_start: 0.8234 (m-40) cc_final: 0.7957 (t0)
REVERT: C  342 MET cc_start: 0.7843 (mmm) cc_final: 0.7506 (mmm)
  outliers start: 3
  outliers final: 0
  residues processed: 447
  average time/residue: 0.1283
  time to fit residues: 83.5465
Evaluate side-chains
  359 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 359
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 138 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 121 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   chunk 172 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 180 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 134 optimal weight:    0.0870
   overall best weight:    3.1764

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 ASN
A 159 GLN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 622 ASN
** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 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 = 0.4215 r_free = 0.4215 target = 0.155471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.118645 restraints weight = 49160.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.122139 restraints weight = 33438.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.124681 restraints weight = 25162.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.126488 restraints weight = 20240.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.127687 restraints weight = 17192.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.5872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16540  Z= 0.200
  Angle     :  0.746  11.957  22255  Z= 0.389
  Chirality :  0.047   0.215   2462
  Planarity :  0.005   0.045   2841
  Dihedral  :  7.264 124.489   2207
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 25.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.40 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.17), residues: 2006
  helix: -0.83 (0.17), residues: 811
  sheet: -2.42 (0.35), residues: 198
  loop : -2.14 (0.19), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 687 
 TYR   0.027   0.002   TYR A 492 
 PHE   0.053   0.002   PHE D 374 
 TRP   0.033   0.002   TRP B 162 
 HIS   0.010   0.001   HIS D 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (16540)
  covalent geometry    : angle       0.74577 (22255)
  hydrogen bonds       : bond        0.04577 (  625)
  hydrogen bonds       : angle       6.06086 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  431 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 429
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8422 (mp0) cc_final: 0.7605 (mp0)
REVERT: D   29 LYS cc_start: 0.9185 (tppt) cc_final: 0.8596 (tttt)
REVERT: D   35 LYS cc_start: 0.9243 (pptt) cc_final: 0.8462 (ttpt)
REVERT: D  102 ILE cc_start: 0.7224 (tp) cc_final: 0.7016 (tp)
REVERT: D  105 LEU cc_start: 0.8507 (mt) cc_final: 0.8255 (mt)
REVERT: D  163 ASN cc_start: 0.8320 (m-40) cc_final: 0.7565 (p0)
REVERT: D  241 LEU cc_start: 0.9473 (mt) cc_final: 0.9265 (mt)
REVERT: D  297 TRP cc_start: 0.8241 (m-10) cc_final: 0.7919 (m-10)
REVERT: D  301 GLU cc_start: 0.9309 (pt0) cc_final: 0.9033 (mp0)
REVERT: D  364 MET cc_start: 0.8691 (tpt) cc_final: 0.8259 (tpp)
REVERT: B   28 GLN cc_start: 0.9174 (pm20) cc_final: 0.8189 (pp30)
REVERT: B   37 PHE cc_start: 0.8678 (m-80) cc_final: 0.8423 (m-80)
REVERT: B   39 SER cc_start: 0.8398 (p) cc_final: 0.8155 (t)
REVERT: B   62 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8762 (tm-30)
REVERT: B  118 PHE cc_start: 0.9515 (t80) cc_final: 0.9258 (t80)
REVERT: B  138 PHE cc_start: 0.8515 (t80) cc_final: 0.8121 (t80)
REVERT: B  203 ILE cc_start: 0.9417 (mt) cc_final: 0.9167 (mt)
REVERT: B  302 ASP cc_start: 0.8788 (m-30) cc_final: 0.8323 (t0)
REVERT: B  345 ARG cc_start: 0.6393 (ttm-80) cc_final: 0.6128 (ttm-80)
REVERT: B  364 TYR cc_start: 0.8705 (m-10) cc_final: 0.8361 (m-10)
REVERT: B  394 LEU cc_start: 0.8862 (mm) cc_final: 0.8602 (mm)
REVERT: B  401 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8690 (mp0)
REVERT: B  419 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7820 (mmtm)
REVERT: B  420 CYS cc_start: 0.8565 (p) cc_final: 0.8348 (p)
REVERT: B  435 LYS cc_start: 0.9116 (pttp) cc_final: 0.8779 (pttm)
REVERT: B  484 MET cc_start: 0.3556 (mmm) cc_final: 0.2869 (mmm)
REVERT: B  510 ARG cc_start: 0.7981 (tpt-90) cc_final: 0.6692 (tpt-90)
REVERT: B  523 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8574 (mp0)
REVERT: B  568 PHE cc_start: 0.9048 (m-10) cc_final: 0.8779 (m-10)
REVERT: B  598 CYS cc_start: 0.8979 (t) cc_final: 0.8715 (t)
REVERT: B  614 MET cc_start: 0.9102 (mtm) cc_final: 0.8868 (mtp)
REVERT: B  621 ASP cc_start: 0.7966 (m-30) cc_final: 0.7699 (m-30)
REVERT: B  647 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7863 (ttp80)
REVERT: A   30 MET cc_start: 0.9057 (ttp) cc_final: 0.8530 (ppp)
REVERT: A   62 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9126 (tp30)
REVERT: A   83 ASN cc_start: 0.8931 (m-40) cc_final: 0.8595 (m-40)
REVERT: A  119 MET cc_start: 0.8901 (tmm) cc_final: 0.8653 (tmm)
REVERT: A  128 ILE cc_start: 0.8717 (mm) cc_final: 0.7889 (mm)
REVERT: A  134 PHE cc_start: 0.8796 (m-10) cc_final: 0.8573 (m-80)
REVERT: A  188 LEU cc_start: 0.8468 (tt) cc_final: 0.7948 (mp)
REVERT: A  194 GLN cc_start: 0.8651 (mp10) cc_final: 0.8175 (mp10)
REVERT: A  200 GLU cc_start: 0.9307 (pm20) cc_final: 0.8786 (pm20)
REVERT: A  213 PHE cc_start: 0.8507 (m-80) cc_final: 0.7399 (m-10)
REVERT: A  306 ASN cc_start: 0.8803 (m-40) cc_final: 0.8438 (p0)
REVERT: A  329 PHE cc_start: 0.8484 (t80) cc_final: 0.8238 (t80)
REVERT: A  361 ILE cc_start: 0.8654 (mm) cc_final: 0.8407 (mm)
REVERT: A  394 LEU cc_start: 0.8937 (mt) cc_final: 0.8511 (mt)
REVERT: A  480 TYR cc_start: 0.8189 (t80) cc_final: 0.7945 (t80)
REVERT: A  509 GLU cc_start: 0.9098 (mp0) cc_final: 0.8821 (mp0)
REVERT: A  521 MET cc_start: 0.8338 (mmp) cc_final: 0.7667 (mmp)
REVERT: A  523 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8757 (mt-10)
REVERT: A  597 CYS cc_start: 0.9147 (m) cc_final: 0.8692 (t)
REVERT: A  604 TYR cc_start: 0.6819 (t80) cc_final: 0.6148 (t80)
REVERT: A  611 GLU cc_start: 0.9532 (tt0) cc_final: 0.9183 (tt0)
REVERT: A  619 LEU cc_start: 0.9426 (mt) cc_final: 0.8952 (mt)
REVERT: A  633 HIS cc_start: 0.8065 (p90) cc_final: 0.7648 (p90)
REVERT: A  636 ILE cc_start: 0.9547 (pt) cc_final: 0.9325 (pt)
REVERT: C  221 MET cc_start: 0.4333 (mmt) cc_final: 0.3994 (mmm)
REVERT: C  342 MET cc_start: 0.7837 (mmm) cc_final: 0.7511 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 430
  average time/residue: 0.1213
  time to fit residues: 76.9744
Evaluate side-chains
  350 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 349
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 131 optimal weight:    0.0980
   chunk 134 optimal weight:    7.9990
   chunk 52 optimal weight:    0.6980
   chunk 21 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 185 optimal weight:    8.9990
   chunk 145 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
D 402 ASN
** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 HIS
B 210 HIS
B 360 ASN
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 HIS
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 HIS
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 345 GLN
** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.158976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.122092 restraints weight = 48628.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.125640 restraints weight = 33296.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.128050 restraints weight = 24822.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.130020 restraints weight = 20028.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.131287 restraints weight = 16887.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.6215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16540  Z= 0.150
  Angle     :  0.720  12.138  22255  Z= 0.371
  Chirality :  0.046   0.188   2462
  Planarity :  0.005   0.061   2841
  Dihedral  :  7.031 123.887   2207
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 20.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.18), residues: 2006
  helix: -0.68 (0.17), residues: 809
  sheet: -2.32 (0.33), residues: 220
  loop : -1.98 (0.19), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 687 
 TYR   0.039   0.002   TYR D 278 
 PHE   0.029   0.002   PHE D 374 
 TRP   0.029   0.002   TRP B 162 
 HIS   0.013   0.001   HIS B 684 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (16540)
  covalent geometry    : angle       0.71969 (22255)
  hydrogen bonds       : bond        0.04151 (  625)
  hydrogen bonds       : angle       5.84311 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  438 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 438
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8193 (mp0) cc_final: 0.7734 (mp0)
REVERT: D   29 LYS cc_start: 0.9183 (tppt) cc_final: 0.8657 (tttt)
REVERT: D  163 ASN cc_start: 0.8299 (m-40) cc_final: 0.7573 (p0)
REVERT: D  297 TRP cc_start: 0.8061 (m-10) cc_final: 0.7742 (m-10)
REVERT: D  301 GLU cc_start: 0.9301 (pt0) cc_final: 0.9069 (pm20)
REVERT: D  364 MET cc_start: 0.8499 (tpt) cc_final: 0.8256 (tpp)
REVERT: D  402 ASN cc_start: 0.7888 (m110) cc_final: 0.7245 (m110)
REVERT: B   28 GLN cc_start: 0.9107 (pm20) cc_final: 0.8295 (pp30)
REVERT: B   37 PHE cc_start: 0.8643 (m-80) cc_final: 0.8368 (m-80)
REVERT: B   39 SER cc_start: 0.8327 (p) cc_final: 0.7811 (t)
REVERT: B   62 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8723 (tm-30)
REVERT: B  118 PHE cc_start: 0.9416 (t80) cc_final: 0.9191 (t80)
REVERT: B  138 PHE cc_start: 0.8352 (t80) cc_final: 0.8136 (t80)
REVERT: B  213 PHE cc_start: 0.8290 (m-80) cc_final: 0.6984 (m-10)
REVERT: B  302 ASP cc_start: 0.8688 (m-30) cc_final: 0.8189 (t0)
REVERT: B  364 TYR cc_start: 0.8566 (m-10) cc_final: 0.8265 (m-10)
REVERT: B  376 GLU cc_start: 0.8891 (mp0) cc_final: 0.8489 (mp0)
REVERT: B  394 LEU cc_start: 0.8852 (mm) cc_final: 0.8603 (mm)
REVERT: B  401 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8549 (mp0)
REVERT: B  419 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7621 (mmtm)
REVERT: B  435 LYS cc_start: 0.9118 (pttp) cc_final: 0.8782 (pttm)
REVERT: B  484 MET cc_start: 0.3723 (mmm) cc_final: 0.3022 (mmm)
REVERT: B  492 TYR cc_start: 0.8896 (m-80) cc_final: 0.8298 (m-80)
REVERT: B  510 ARG cc_start: 0.7855 (tpt-90) cc_final: 0.6582 (tpt-90)
REVERT: B  523 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8530 (mp0)
REVERT: B  568 PHE cc_start: 0.9055 (m-10) cc_final: 0.8812 (m-10)
REVERT: B  598 CYS cc_start: 0.9021 (t) cc_final: 0.8708 (t)
REVERT: B  620 ARG cc_start: 0.8073 (tmt-80) cc_final: 0.7785 (tpt90)
REVERT: B  621 ASP cc_start: 0.7781 (m-30) cc_final: 0.7279 (m-30)
REVERT: B  622 ASN cc_start: 0.7483 (m110) cc_final: 0.7125 (m110)
REVERT: B  647 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.7792 (ttp80)
REVERT: A   83 ASN cc_start: 0.8938 (m-40) cc_final: 0.8614 (m-40)
REVERT: A  119 MET cc_start: 0.8870 (tmm) cc_final: 0.8636 (tmm)
REVERT: A  128 ILE cc_start: 0.8729 (mm) cc_final: 0.7979 (mm)
REVERT: A  180 MET cc_start: 0.9148 (mtm) cc_final: 0.8623 (mtt)
REVERT: A  194 GLN cc_start: 0.8597 (mp10) cc_final: 0.8138 (mp10)
REVERT: A  200 GLU cc_start: 0.9222 (pm20) cc_final: 0.8700 (pm20)
REVERT: A  213 PHE cc_start: 0.8374 (m-80) cc_final: 0.7141 (m-10)
REVERT: A  306 ASN cc_start: 0.8760 (m-40) cc_final: 0.8432 (p0)
REVERT: A  314 LYS cc_start: 0.9216 (mmtt) cc_final: 0.8674 (mmtt)
REVERT: A  329 PHE cc_start: 0.8442 (t80) cc_final: 0.8222 (t80)
REVERT: A  342 PHE cc_start: 0.8464 (m-80) cc_final: 0.7866 (m-80)
REVERT: A  361 ILE cc_start: 0.8507 (mm) cc_final: 0.8207 (mm)
REVERT: A  394 LEU cc_start: 0.8905 (mt) cc_final: 0.8502 (mt)
REVERT: A  509 GLU cc_start: 0.9087 (mp0) cc_final: 0.8766 (mp0)
REVERT: A  521 MET cc_start: 0.8314 (mmp) cc_final: 0.7662 (mmp)
REVERT: A  523 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8745 (mt-10)
REVERT: A  597 CYS cc_start: 0.9134 (m) cc_final: 0.8716 (t)
REVERT: A  604 TYR cc_start: 0.6470 (t80) cc_final: 0.5837 (t80)
REVERT: A  614 MET cc_start: 0.8963 (mtm) cc_final: 0.8582 (mtp)
REVERT: A  628 MET cc_start: 0.5205 (mmm) cc_final: 0.4574 (mmm)
REVERT: A  633 HIS cc_start: 0.7951 (p90) cc_final: 0.7594 (p90)
REVERT: A  636 ILE cc_start: 0.9531 (pt) cc_final: 0.9316 (pt)
REVERT: C  221 MET cc_start: 0.4304 (mmt) cc_final: 0.3947 (mmm)
REVERT: C  292 LEU cc_start: 0.9057 (pt) cc_final: 0.8837 (pp)
REVERT: C  331 VAL cc_start: 0.7875 (t) cc_final: 0.7383 (t)
REVERT: C  332 ASN cc_start: 0.8150 (m-40) cc_final: 0.7861 (t0)
REVERT: C  342 MET cc_start: 0.7916 (mmm) cc_final: 0.7604 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 438
  average time/residue: 0.1152
  time to fit residues: 74.2927
Evaluate side-chains
  361 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 361
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 164 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 185 optimal weight:   10.0000
   chunk 171 optimal weight:    0.9980
   chunk 38 optimal weight:   20.0000
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
D 322 ASN
** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 HIS
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 404 GLN
B 684 HIS
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 HIS
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.155910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.118791 restraints weight = 49410.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.122160 restraints weight = 34206.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.124494 restraints weight = 25704.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.126310 restraints weight = 20848.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.127670 restraints weight = 17767.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.6494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  16540  Z= 0.182
  Angle     :  0.767  11.765  22255  Z= 0.398
  Chirality :  0.048   0.376   2462
  Planarity :  0.005   0.049   2841
  Dihedral  :  7.171 127.662   2207
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 23.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.18), residues: 2006
  helix: -0.70 (0.17), residues: 802
  sheet: -2.13 (0.35), residues: 202
  loop : -1.97 (0.19), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 357 
 TYR   0.029   0.002   TYR A 492 
 PHE   0.051   0.003   PHE B  37 
 TRP   0.028   0.002   TRP A 162 
 HIS   0.020   0.002   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (16540)
  covalent geometry    : angle       0.76703 (22255)
  hydrogen bonds       : bond        0.04361 (  625)
  hydrogen bonds       : angle       5.94802 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 428
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8449 (mp0) cc_final: 0.7949 (mp0)
REVERT: D   29 LYS cc_start: 0.9188 (tppt) cc_final: 0.8670 (tttt)
REVERT: D  163 ASN cc_start: 0.8337 (m-40) cc_final: 0.7582 (p0)
REVERT: D  297 TRP cc_start: 0.8250 (m-10) cc_final: 0.7884 (m-10)
REVERT: D  301 GLU cc_start: 0.9326 (pt0) cc_final: 0.9092 (pm20)
REVERT: D  364 MET cc_start: 0.8529 (tpt) cc_final: 0.8280 (tpp)
REVERT: B   28 GLN cc_start: 0.9043 (pm20) cc_final: 0.8498 (pp30)
REVERT: B   39 SER cc_start: 0.8345 (p) cc_final: 0.7869 (t)
REVERT: B   62 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8689 (tm-30)
REVERT: B  118 PHE cc_start: 0.9479 (t80) cc_final: 0.9246 (t80)
REVERT: B  138 PHE cc_start: 0.8651 (t80) cc_final: 0.8237 (t80)
REVERT: B  139 TYR cc_start: 0.8667 (m-10) cc_final: 0.8462 (m-10)
REVERT: B  203 ILE cc_start: 0.9387 (mt) cc_final: 0.9149 (mt)
REVERT: B  213 PHE cc_start: 0.8329 (m-80) cc_final: 0.6937 (m-10)
REVERT: B  302 ASP cc_start: 0.8775 (m-30) cc_final: 0.8233 (t0)
REVERT: B  345 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.6386 (ttm170)
REVERT: B  364 TYR cc_start: 0.8675 (m-10) cc_final: 0.8378 (m-10)
REVERT: B  394 LEU cc_start: 0.8863 (mm) cc_final: 0.8588 (mm)
REVERT: B  401 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8834 (mp0)
REVERT: B  435 LYS cc_start: 0.9105 (pttp) cc_final: 0.8799 (pttm)
REVERT: B  474 MET cc_start: 0.9278 (mmm) cc_final: 0.9012 (mmm)
REVERT: B  484 MET cc_start: 0.3786 (mmm) cc_final: 0.2863 (mmm)
REVERT: B  495 THR cc_start: 0.8391 (p) cc_final: 0.8172 (p)
REVERT: B  510 ARG cc_start: 0.7881 (tpt-90) cc_final: 0.6595 (tpt-90)
REVERT: B  523 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8628 (mp0)
REVERT: B  540 THR cc_start: 0.8823 (t) cc_final: 0.8489 (m)
REVERT: B  568 PHE cc_start: 0.9120 (m-10) cc_final: 0.8834 (m-10)
REVERT: B  598 CYS cc_start: 0.9082 (t) cc_final: 0.8796 (t)
REVERT: B  620 ARG cc_start: 0.8166 (tmt-80) cc_final: 0.7953 (tpt90)
REVERT: B  647 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.7837 (ttp80)
REVERT: B  668 GLU cc_start: 0.8813 (pp20) cc_final: 0.8592 (pp20)
REVERT: A   62 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9095 (tp30)
REVERT: A   83 ASN cc_start: 0.8952 (m-40) cc_final: 0.8611 (m-40)
REVERT: A  119 MET cc_start: 0.8803 (tmm) cc_final: 0.8565 (tmm)
REVERT: A  180 MET cc_start: 0.9117 (mtm) cc_final: 0.8857 (mtm)
REVERT: A  188 LEU cc_start: 0.8466 (tt) cc_final: 0.7840 (mp)
REVERT: A  194 GLN cc_start: 0.8642 (mp10) cc_final: 0.8229 (mp10)
REVERT: A  200 GLU cc_start: 0.9230 (pm20) cc_final: 0.8759 (pm20)
REVERT: A  213 PHE cc_start: 0.8393 (m-80) cc_final: 0.7373 (m-10)
REVERT: A  306 ASN cc_start: 0.8920 (m-40) cc_final: 0.8591 (p0)
REVERT: A  314 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8720 (mmtt)
REVERT: A  361 ILE cc_start: 0.8420 (mm) cc_final: 0.8109 (mm)
REVERT: A  394 LEU cc_start: 0.8963 (mt) cc_final: 0.8547 (mt)
REVERT: A  396 LEU cc_start: 0.9464 (mt) cc_final: 0.9044 (pp)
REVERT: A  480 TYR cc_start: 0.8184 (t80) cc_final: 0.7901 (t80)
REVERT: A  509 GLU cc_start: 0.9095 (mp0) cc_final: 0.8782 (mp0)
REVERT: A  521 MET cc_start: 0.8335 (mmp) cc_final: 0.7606 (mmp)
REVERT: A  523 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8750 (mt-10)
REVERT: A  597 CYS cc_start: 0.9187 (m) cc_final: 0.8778 (t)
REVERT: A  604 TYR cc_start: 0.6615 (t80) cc_final: 0.6122 (t80)
REVERT: A  614 MET cc_start: 0.9040 (mtm) cc_final: 0.8547 (mtp)
REVERT: A  619 LEU cc_start: 0.9509 (mt) cc_final: 0.9069 (mt)
REVERT: A  620 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8523 (mmm160)
REVERT: A  633 HIS cc_start: 0.7963 (p90) cc_final: 0.7609 (p90)
REVERT: A  636 ILE cc_start: 0.9554 (pt) cc_final: 0.9346 (pt)
REVERT: C  221 MET cc_start: 0.4061 (mmt) cc_final: 0.3692 (mmm)
REVERT: C  292 LEU cc_start: 0.9068 (pt) cc_final: 0.8831 (pp)
REVERT: C  342 MET cc_start: 0.7748 (mmm) cc_final: 0.7398 (mmm)
REVERT: C  554 MET cc_start: 0.8288 (tmm) cc_final: 0.7764 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 428
  average time/residue: 0.1152
  time to fit residues: 73.0684
Evaluate side-chains
  343 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 343
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 147 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 190 optimal weight:    0.0470
   chunk 102 optimal weight:    0.7980
   chunk 158 optimal weight:    3.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
D 365 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
C 304 HIS
C 367 ASN
** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.161725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.125505 restraints weight = 48537.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.129079 restraints weight = 33185.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.131802 restraints weight = 24713.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.133772 restraints weight = 19599.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.135056 restraints weight = 16364.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.6770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16540  Z= 0.137
  Angle     :  0.746  12.344  22255  Z= 0.381
  Chirality :  0.046   0.280   2462
  Planarity :  0.004   0.050   2841
  Dihedral  :  6.846 122.568   2207
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.30 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.18), residues: 2006
  helix: -0.60 (0.17), residues: 795
  sheet: -1.89 (0.35), residues: 202
  loop : -1.90 (0.19), residues: 1009

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 687 
 TYR   0.040   0.002   TYR D 278 
 PHE   0.050   0.002   PHE A  37 
 TRP   0.026   0.002   TRP A 162 
 HIS   0.013   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (16540)
  covalent geometry    : angle       0.74575 (22255)
  hydrogen bonds       : bond        0.04187 (  625)
  hydrogen bonds       : angle       5.69882 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  451 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 449
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8196 (mp0) cc_final: 0.7802 (mp0)
REVERT: D   29 LYS cc_start: 0.9143 (tppt) cc_final: 0.8628 (tttt)
REVERT: D  130 PHE cc_start: 0.5822 (p90) cc_final: 0.5293 (p90)
REVERT: D  131 GLU cc_start: 0.7477 (tp30) cc_final: 0.7020 (tp30)
REVERT: D  163 ASN cc_start: 0.8326 (m-40) cc_final: 0.7629 (p0)
REVERT: D  301 GLU cc_start: 0.9319 (pt0) cc_final: 0.9089 (pm20)
REVERT: D  351 GLU cc_start: 0.8575 (mp0) cc_final: 0.8062 (tm-30)
REVERT: D  364 MET cc_start: 0.8580 (tpt) cc_final: 0.8301 (tpp)
REVERT: B   28 GLN cc_start: 0.9010 (pm20) cc_final: 0.8480 (pp30)
REVERT: B   39 SER cc_start: 0.8178 (p) cc_final: 0.7707 (t)
REVERT: B   62 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8685 (tm-30)
REVERT: B   98 MET cc_start: 0.7023 (pmm) cc_final: 0.5949 (pmm)
REVERT: B  118 PHE cc_start: 0.9453 (t80) cc_final: 0.9226 (t80)
REVERT: B  138 PHE cc_start: 0.8599 (t80) cc_final: 0.8189 (t80)
REVERT: B  180 MET cc_start: 0.8186 (mtm) cc_final: 0.7816 (ptp)
REVERT: B  191 LYS cc_start: 0.9053 (pttp) cc_final: 0.8744 (pttm)
REVERT: B  345 ARG cc_start: 0.6422 (ttm-80) cc_final: 0.5387 (ttm110)
REVERT: B  394 LEU cc_start: 0.8877 (mm) cc_final: 0.8661 (mm)
REVERT: B  401 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8717 (mp0)
REVERT: B  435 LYS cc_start: 0.9109 (pttp) cc_final: 0.8784 (pttm)
REVERT: B  474 MET cc_start: 0.9315 (mmm) cc_final: 0.9065 (mmm)
REVERT: B  484 MET cc_start: 0.3709 (mmm) cc_final: 0.2758 (mmm)
REVERT: B  492 TYR cc_start: 0.8930 (m-80) cc_final: 0.8363 (m-80)
REVERT: B  536 PHE cc_start: 0.8096 (t80) cc_final: 0.6957 (t80)
REVERT: B  547 GLU cc_start: 0.8841 (pt0) cc_final: 0.7949 (pt0)
REVERT: B  579 LEU cc_start: 0.9419 (mt) cc_final: 0.9206 (pp)
REVERT: B  598 CYS cc_start: 0.9043 (t) cc_final: 0.8776 (t)
REVERT: B  647 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.7841 (ttp80)
REVERT: A   83 ASN cc_start: 0.8887 (m-40) cc_final: 0.8533 (m-40)
REVERT: A  119 MET cc_start: 0.8816 (tmm) cc_final: 0.8588 (tmm)
REVERT: A  180 MET cc_start: 0.9143 (mtm) cc_final: 0.8702 (mtt)
REVERT: A  188 LEU cc_start: 0.8499 (tt) cc_final: 0.7896 (mp)
REVERT: A  194 GLN cc_start: 0.8513 (mp10) cc_final: 0.8122 (mp10)
REVERT: A  200 GLU cc_start: 0.9170 (pm20) cc_final: 0.8667 (pm20)
REVERT: A  213 PHE cc_start: 0.8326 (m-80) cc_final: 0.6953 (m-10)
REVERT: A  306 ASN cc_start: 0.8807 (m-40) cc_final: 0.8464 (p0)
REVERT: A  314 LYS cc_start: 0.9306 (mmtt) cc_final: 0.8754 (mmtt)
REVERT: A  342 PHE cc_start: 0.8496 (m-80) cc_final: 0.7919 (m-80)
REVERT: A  361 ILE cc_start: 0.8274 (mm) cc_final: 0.7883 (mm)
REVERT: A  394 LEU cc_start: 0.8952 (mt) cc_final: 0.8541 (mt)
REVERT: A  396 LEU cc_start: 0.9402 (mt) cc_final: 0.8919 (pp)
REVERT: A  458 LYS cc_start: 0.9128 (mppt) cc_final: 0.8909 (mppt)
REVERT: A  480 TYR cc_start: 0.8214 (t80) cc_final: 0.7892 (t80)
REVERT: A  509 GLU cc_start: 0.9224 (mp0) cc_final: 0.8831 (pm20)
REVERT: A  522 ILE cc_start: 0.8811 (pt) cc_final: 0.8495 (mt)
REVERT: A  523 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8710 (mt-10)
REVERT: A  597 CYS cc_start: 0.9106 (m) cc_final: 0.8705 (t)
REVERT: A  614 MET cc_start: 0.8968 (mtm) cc_final: 0.8562 (mtp)
REVERT: A  628 MET cc_start: 0.4979 (mmm) cc_final: 0.4674 (mmm)
REVERT: A  633 HIS cc_start: 0.7837 (p90) cc_final: 0.7541 (p90)
REVERT: A  636 ILE cc_start: 0.9550 (pt) cc_final: 0.9153 (pt)
REVERT: C  221 MET cc_start: 0.3652 (mmt) cc_final: 0.3279 (mmm)
REVERT: C  292 LEU cc_start: 0.9048 (pt) cc_final: 0.8814 (pp)
REVERT: C  331 VAL cc_start: 0.7885 (t) cc_final: 0.7491 (t)
REVERT: C  342 MET cc_start: 0.7885 (mmm) cc_final: 0.7556 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 450
  average time/residue: 0.1148
  time to fit residues: 75.8753
Evaluate side-chains
  364 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 364
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 154 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 174 optimal weight:    0.0670
   chunk 51 optimal weight:    0.0870
   chunk 132 optimal weight:   10.0000
   chunk 175 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 179 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 190 optimal weight:    0.9980
   overall best weight:    0.5896

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

Flipped N/Q/H residues before XYZ refinement:
D 322 ASN
** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS
A 531 GLN
** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.163561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.127026 restraints weight = 48546.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.130793 restraints weight = 32880.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.133534 restraints weight = 24435.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.135471 restraints weight = 19381.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.136954 restraints weight = 16223.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.7052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16540  Z= 0.135
  Angle     :  0.741  12.297  22255  Z= 0.378
  Chirality :  0.046   0.255   2462
  Planarity :  0.004   0.050   2841
  Dihedral  :  6.664 119.829   2207
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.62 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.18), residues: 2006
  helix: -0.57 (0.17), residues: 799
  sheet: -1.67 (0.35), residues: 202
  loop : -1.84 (0.19), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 687 
 TYR   0.034   0.002   TYR A 465 
 PHE   0.039   0.002   PHE A  37 
 TRP   0.032   0.002   TRP A 162 
 HIS   0.009   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (16540)
  covalent geometry    : angle       0.74109 (22255)
  hydrogen bonds       : bond        0.04005 (  625)
  hydrogen bonds       : angle       5.58955 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  457 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 456
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8121 (mp0) cc_final: 0.7656 (mp0)
REVERT: D   29 LYS cc_start: 0.9083 (tppt) cc_final: 0.8544 (tttt)
REVERT: D   35 LYS cc_start: 0.9186 (pptt) cc_final: 0.8689 (tmmt)
REVERT: D  130 PHE cc_start: 0.5706 (p90) cc_final: 0.5351 (p90)
REVERT: D  163 ASN cc_start: 0.8359 (m-40) cc_final: 0.7571 (p0)
REVERT: D  364 MET cc_start: 0.8565 (tpt) cc_final: 0.8262 (tpp)
REVERT: B   28 GLN cc_start: 0.8946 (pm20) cc_final: 0.8375 (pp30)
REVERT: B   39 SER cc_start: 0.7879 (p) cc_final: 0.7329 (t)
REVERT: B   62 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8685 (tm-30)
REVERT: B   98 MET cc_start: 0.7061 (pmm) cc_final: 0.6066 (pmm)
REVERT: B  118 PHE cc_start: 0.9406 (t80) cc_final: 0.9175 (t80)
REVERT: B  138 PHE cc_start: 0.8543 (t80) cc_final: 0.8182 (t80)
REVERT: B  163 GLU cc_start: 0.8440 (pm20) cc_final: 0.6693 (tm-30)
REVERT: B  191 LYS cc_start: 0.9002 (pttp) cc_final: 0.8673 (pttm)
REVERT: B  345 ARG cc_start: 0.6383 (ttm-80) cc_final: 0.5379 (ttm110)
REVERT: B  376 GLU cc_start: 0.8784 (mp0) cc_final: 0.8547 (mp0)
REVERT: B  394 LEU cc_start: 0.8889 (mm) cc_final: 0.8640 (mm)
REVERT: B  401 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8616 (mp0)
REVERT: B  435 LYS cc_start: 0.9100 (pttp) cc_final: 0.8754 (pttm)
REVERT: B  474 MET cc_start: 0.9341 (mmm) cc_final: 0.9105 (mmm)
REVERT: B  484 MET cc_start: 0.3659 (mmm) cc_final: 0.2527 (mmm)
REVERT: B  492 TYR cc_start: 0.8953 (m-80) cc_final: 0.8410 (m-80)
REVERT: B  537 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7659 (tm-30)
REVERT: B  579 LEU cc_start: 0.9405 (mt) cc_final: 0.9187 (pp)
REVERT: B  598 CYS cc_start: 0.9046 (t) cc_final: 0.8837 (t)
REVERT: B  647 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.7826 (ttp80)
REVERT: A   66 ASP cc_start: 0.6740 (t70) cc_final: 0.5978 (t0)
REVERT: A   83 ASN cc_start: 0.8858 (m-40) cc_final: 0.8517 (m-40)
REVERT: A  119 MET cc_start: 0.8723 (tmm) cc_final: 0.8398 (tmm)
REVERT: A  120 GLU cc_start: 0.8932 (pt0) cc_final: 0.8596 (pt0)
REVERT: A  188 LEU cc_start: 0.8501 (tt) cc_final: 0.7931 (mp)
REVERT: A  194 GLN cc_start: 0.8485 (mp10) cc_final: 0.8058 (mp10)
REVERT: A  200 GLU cc_start: 0.9159 (pm20) cc_final: 0.8778 (pm20)
REVERT: A  213 PHE cc_start: 0.8278 (m-80) cc_final: 0.6960 (m-10)
REVERT: A  224 LYS cc_start: 0.7165 (pttm) cc_final: 0.6652 (mttt)
REVERT: A  306 ASN cc_start: 0.8770 (m-40) cc_final: 0.8387 (p0)
REVERT: A  314 LYS cc_start: 0.9319 (mmtt) cc_final: 0.8793 (mmtt)
REVERT: A  342 PHE cc_start: 0.8510 (m-80) cc_final: 0.7957 (m-80)
REVERT: A  394 LEU cc_start: 0.8954 (mt) cc_final: 0.8543 (mt)
REVERT: A  396 LEU cc_start: 0.9375 (mt) cc_final: 0.8877 (pp)
REVERT: A  458 LYS cc_start: 0.9182 (mppt) cc_final: 0.8957 (mppt)
REVERT: A  480 TYR cc_start: 0.8220 (t80) cc_final: 0.7889 (t80)
REVERT: A  509 GLU cc_start: 0.9064 (mp0) cc_final: 0.8606 (pm20)
REVERT: A  514 HIS cc_start: 0.8284 (m90) cc_final: 0.8020 (m90)
REVERT: A  523 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8668 (mt-10)
REVERT: A  597 CYS cc_start: 0.9084 (m) cc_final: 0.8740 (t)
REVERT: A  614 MET cc_start: 0.8981 (mtm) cc_final: 0.8571 (mtp)
REVERT: A  619 LEU cc_start: 0.9512 (mt) cc_final: 0.9084 (mt)
REVERT: A  620 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8555 (mmm160)
REVERT: A  633 HIS cc_start: 0.7717 (p90) cc_final: 0.7510 (p90)
REVERT: A  636 ILE cc_start: 0.9551 (pt) cc_final: 0.9168 (pt)
REVERT: C  221 MET cc_start: 0.3612 (mmt) cc_final: 0.3348 (mmm)
REVERT: C  292 LEU cc_start: 0.9100 (pt) cc_final: 0.8865 (pp)
REVERT: C  342 MET cc_start: 0.7990 (mmm) cc_final: 0.7640 (mmm)
REVERT: C  554 MET cc_start: 0.8251 (tmm) cc_final: 0.7860 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 457
  average time/residue: 0.1039
  time to fit residues: 70.5600
Evaluate side-chains
  363 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 363
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 152 optimal weight:    9.9990
   chunk 84 optimal weight:    0.8980
   chunk 129 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 177 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 131 optimal weight:    0.4980
   chunk 178 optimal weight:    6.9990
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 617 GLN
B 622 ASN
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
A 490 HIS
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 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 = 0.4269 r_free = 0.4269 target = 0.160227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.123621 restraints weight = 49071.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.127153 restraints weight = 33737.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.129756 restraints weight = 25257.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.131645 restraints weight = 20180.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.132861 restraints weight = 16976.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.7200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  16540  Z= 0.154
  Angle     :  0.778  11.541  22255  Z= 0.400
  Chirality :  0.047   0.256   2462
  Planarity :  0.004   0.054   2841
  Dihedral  :  6.811 124.218   2207
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.18), residues: 2006
  helix: -0.63 (0.17), residues: 812
  sheet: -1.72 (0.34), residues: 202
  loop : -1.85 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 687 
 TYR   0.041   0.002   TYR D 278 
 PHE   0.028   0.002   PHE D 374 
 TRP   0.046   0.002   TRP D 297 
 HIS   0.012   0.002   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (16540)
  covalent geometry    : angle       0.77814 (22255)
  hydrogen bonds       : bond        0.04227 (  625)
  hydrogen bonds       : angle       5.70643 ( 1752)

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

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

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4012 Ramachandran restraints generated.
    2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 434
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   23 GLU cc_start: 0.8109 (mp0) cc_final: 0.7523 (mp0)
REVERT: D   29 LYS cc_start: 0.9072 (tppt) cc_final: 0.8559 (tttt)
REVERT: D   35 LYS cc_start: 0.9169 (pptt) cc_final: 0.8706 (tmmt)
REVERT: D  163 ASN cc_start: 0.8303 (m-40) cc_final: 0.7593 (p0)
REVERT: D  203 ASP cc_start: 0.9270 (p0) cc_final: 0.8454 (m-30)
REVERT: D  350 ASN cc_start: 0.8953 (p0) cc_final: 0.8555 (p0)
REVERT: D  351 GLU cc_start: 0.8625 (mp0) cc_final: 0.8238 (tm-30)
REVERT: D  364 MET cc_start: 0.8566 (tpt) cc_final: 0.8212 (tpp)
REVERT: B   28 GLN cc_start: 0.8974 (pm20) cc_final: 0.8500 (pp30)
REVERT: B   62 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8669 (tm-30)
REVERT: B   98 MET cc_start: 0.7171 (pmm) cc_final: 0.6127 (pmm)
REVERT: B  118 PHE cc_start: 0.9368 (t80) cc_final: 0.9147 (t80)
REVERT: B  175 ASP cc_start: 0.8125 (t0) cc_final: 0.7888 (t0)
REVERT: B  182 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7456 (mtt-85)
REVERT: B  345 ARG cc_start: 0.6535 (ttm-80) cc_final: 0.5437 (ttm110)
REVERT: B  376 GLU cc_start: 0.8803 (mp0) cc_final: 0.8554 (mp0)
REVERT: B  394 LEU cc_start: 0.8875 (mm) cc_final: 0.8594 (mm)
REVERT: B  401 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8713 (mp0)
REVERT: B  435 LYS cc_start: 0.9133 (pttp) cc_final: 0.8769 (pttm)
REVERT: B  474 MET cc_start: 0.9287 (mmm) cc_final: 0.9041 (mmm)
REVERT: B  492 TYR cc_start: 0.8935 (m-80) cc_final: 0.8422 (m-80)
REVERT: B  526 ASP cc_start: 0.8384 (t0) cc_final: 0.7946 (t0)
REVERT: B  530 VAL cc_start: 0.8397 (m) cc_final: 0.8075 (m)
REVERT: B  536 PHE cc_start: 0.7630 (t80) cc_final: 0.6061 (t80)
REVERT: B  568 PHE cc_start: 0.9125 (m-10) cc_final: 0.8730 (m-10)
REVERT: B  598 CYS cc_start: 0.9091 (t) cc_final: 0.8850 (t)
REVERT: B  647 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.7840 (ttp80)
REVERT: A   83 ASN cc_start: 0.8937 (m-40) cc_final: 0.8592 (m-40)
REVERT: A  119 MET cc_start: 0.8689 (tmm) cc_final: 0.8410 (tmm)
REVERT: A  120 GLU cc_start: 0.8957 (pt0) cc_final: 0.8595 (pt0)
REVERT: A  188 LEU cc_start: 0.8535 (tt) cc_final: 0.7870 (mp)
REVERT: A  194 GLN cc_start: 0.8445 (mp10) cc_final: 0.8079 (mp10)
REVERT: A  200 GLU cc_start: 0.9132 (pm20) cc_final: 0.8669 (pm20)
REVERT: A  213 PHE cc_start: 0.8244 (m-80) cc_final: 0.7211 (m-10)
REVERT: A  306 ASN cc_start: 0.8736 (m-40) cc_final: 0.8423 (p0)
REVERT: A  314 LYS cc_start: 0.9303 (mmtt) cc_final: 0.8779 (mmtt)
REVERT: A  342 PHE cc_start: 0.8453 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  361 ILE cc_start: 0.8383 (mm) cc_final: 0.8093 (mm)
REVERT: A  394 LEU cc_start: 0.8963 (mt) cc_final: 0.8551 (mt)
REVERT: A  396 LEU cc_start: 0.9410 (mt) cc_final: 0.8951 (pp)
REVERT: A  458 LYS cc_start: 0.9133 (mppt) cc_final: 0.8928 (mppt)
REVERT: A  480 TYR cc_start: 0.8000 (t80) cc_final: 0.7706 (t80)
REVERT: A  509 GLU cc_start: 0.9018 (mp0) cc_final: 0.8571 (pm20)
REVERT: A  597 CYS cc_start: 0.9061 (m) cc_final: 0.8729 (t)
REVERT: A  614 MET cc_start: 0.8887 (mtm) cc_final: 0.8564 (mtp)
REVERT: A  619 LEU cc_start: 0.9488 (mt) cc_final: 0.9046 (mt)
REVERT: A  620 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8562 (mmm160)
REVERT: C  221 MET cc_start: 0.3650 (mmt) cc_final: 0.3411 (mmm)
REVERT: C  292 LEU cc_start: 0.9065 (pt) cc_final: 0.8830 (pp)
REVERT: C  342 MET cc_start: 0.7917 (mmm) cc_final: 0.7575 (mmm)
REVERT: C  554 MET cc_start: 0.7917 (tmm) cc_final: 0.7516 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 434
  average time/residue: 0.1107
  time to fit residues: 70.9499
Evaluate side-chains
  349 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 349
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 145 optimal weight:    0.4980
   chunk 7 optimal weight:    7.9990
   chunk 163 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 180 optimal weight:    5.9990
   chunk 196 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 127 optimal weight:    0.8980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
D  71 HIS
D 322 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 622 ASN
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
A 490 HIS
A 504 ASN
** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.159663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.122627 restraints weight = 48520.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.126207 restraints weight = 33207.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.128665 restraints weight = 24937.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.130523 restraints weight = 20090.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.131737 restraints weight = 16999.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.7325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  16540  Z= 0.155
  Angle     :  0.774  11.420  22255  Z= 0.398
  Chirality :  0.046   0.245   2462
  Planarity :  0.004   0.052   2841
  Dihedral  :  6.834 124.826   2207
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.18), residues: 2006
  helix: -0.64 (0.17), residues: 801
  sheet: -1.78 (0.33), residues: 221
  loop : -1.87 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 687 
 TYR   0.021   0.002   TYR D 278 
 PHE   0.051   0.002   PHE A  37 
 TRP   0.023   0.002   TRP A 162 
 HIS   0.014   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (16540)
  covalent geometry    : angle       0.77426 (22255)
  hydrogen bonds       : bond        0.04057 (  625)
  hydrogen bonds       : angle       5.71025 ( 1752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3022.04 seconds
wall clock time: 53 minutes 12.51 seconds (3192.51 seconds total)