Starting phenix.real_space_refine
on Fri Aug 22 17:27:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wk6_32560/08_2025/7wk6_32560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wk6_32560/08_2025/7wk6_32560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wk6_32560/08_2025/7wk6_32560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wk6_32560/08_2025/7wk6_32560.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wk6_32560/08_2025/7wk6_32560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wk6_32560/08_2025/7wk6_32560.map"
  }
  resolution = 3.67
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4119      2.51       5
     N    1069      2.21       5
     O    1203      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6428
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "E"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1558
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
  Time building chain proxies: 1.73, per 1000 atoms: 0.27
  Number of scatterers: 6428
  At special positions: 0
  Unit cell: (76.51, 99.463, 113.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1203      8.00
     N    1069      7.00
     C    4119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.06
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 352.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      47.7% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'E' and resid 349 through 353
      removed outlier: 4.154A  pdb=" N   TRP E 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 364 through 372
      removed outlier: 4.096A  pdb=" N   LEU E 368 " --> pdb=" O   ASP E 364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 417 through 422
    Processing helix  chain 'A' and resid 20 through 49
      removed outlier: 3.770A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA A  46 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 4.025A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LYS A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TRP A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLU A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 90 through 98
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.680A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
      removed outlier: 3.662A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 176 through 192
      removed outlier: 3.707A  pdb=" N   GLU A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TYR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 219 through 231
      removed outlier: 4.243A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 248
      removed outlier: 3.508A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 298
      removed outlier: 3.577A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 316
      removed outlier: 3.961A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.637A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 383
      removed outlier: 3.956A  pdb=" N   THR A 371 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   HIS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 4.463A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 412
      removed outlier: 3.549A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 412 " --> pdb=" O   MET A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'A' and resid 434 through 447
      removed outlier: 3.532A  pdb=" N   PHE A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.211A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU A 456 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.627A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 3.817A  pdb=" N   SER A 502 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.707A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 523
      removed outlier: 3.831A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 533
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.755A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.615A  pdb=" N   GLN A 552 " --> pdb=" O   THR A 548 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 572
      removed outlier: 3.574A  pdb=" N   GLU A 571 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.514A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.810A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL E 433 " --> pdb=" O   LYS E 378 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS E 378 " --> pdb=" O   VAL E 433 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.158A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.396A  pdb=" N   ALA A 348 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LEU A 359 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   ASP A 350 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ARG A 357 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY A 352 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)

    200 hydrogen bonds defined for protein.
    555 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1106
        1.32 -     1.45: 1931
        1.45 -     1.58: 3516
        1.58 -     1.71: 0
        1.71 -     1.84: 58
  Bond restraints: 6611
  Sorted by residual:
  bond pdb=" CA  SER E 366 "
       pdb=" C   SER E 366 "
    ideal  model  delta    sigma   weight residual
    1.523  1.436  0.087 1.30e-02 5.92e+03 4.52e+01
  bond pdb=" CA  LYS A  31 "
       pdb=" C   LYS A  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.454  0.070 1.26e-02 6.30e+03 3.09e+01
  bond pdb=" CA  TYR E 365 "
       pdb=" C   TYR E 365 "
    ideal  model  delta    sigma   weight residual
    1.522  1.449  0.073 1.41e-02 5.03e+03 2.67e+01
  bond pdb=" CA  ASN A  33 "
       pdb=" C   ASN A  33 "
    ideal  model  delta    sigma   weight residual
    1.524  1.460  0.064 1.27e-02 6.20e+03 2.51e+01
  bond pdb=" CA  GLU A  35 "
       pdb=" CB  GLU A  35 "
    ideal  model  delta    sigma   weight residual
    1.528  1.452  0.077 1.59e-02 3.96e+03 2.33e+01
  ... (remaining 6606 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 8820
        3.26 -     6.52: 139
        6.52 -     9.78: 20
        9.78 -    13.05: 4
       13.05 -    16.31: 3
  Bond angle restraints: 8986
  Sorted by residual:
  angle pdb=" N   CYS A 141 "
        pdb=" CA  CYS A 141 "
        pdb=" C   CYS A 141 "
      ideal   model   delta    sigma   weight residual
     109.29  122.96  -13.67 1.41e+00 5.03e-01 9.40e+01
  angle pdb=" N   CYS E 488 "
        pdb=" CA  CYS E 488 "
        pdb=" C   CYS E 488 "
      ideal   model   delta    sigma   weight residual
     107.20   90.89   16.31 1.70e+00 3.46e-01 9.20e+01
  angle pdb=" N   LEU A 142 "
        pdb=" CA  LEU A 142 "
        pdb=" C   LEU A 142 "
      ideal   model   delta    sigma   weight residual
     109.50  124.40  -14.90 1.58e+00 4.01e-01 8.89e+01
  angle pdb=" N   LEU E 371 "
        pdb=" CA  LEU E 371 "
        pdb=" C   LEU E 371 "
      ideal   model   delta    sigma   weight residual
     113.20  103.39    9.81 1.21e+00 6.83e-01 6.57e+01
  angle pdb=" N   PRO E 373 "
        pdb=" CA  PRO E 373 "
        pdb=" C   PRO E 373 "
      ideal   model   delta    sigma   weight residual
     113.53  102.47   11.06 1.39e+00 5.18e-01 6.33e+01
  ... (remaining 8981 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.99: 3458
       18.99 -    37.99: 372
       37.99 -    56.98: 59
       56.98 -    75.97: 12
       75.97 -    94.97: 4
  Dihedral angle restraints: 3905
    sinusoidal: 1579
      harmonic: 2326
  Sorted by residual:
  dihedral pdb=" CA  GLU A 145 "
           pdb=" C   GLU A 145 "
           pdb=" N   PRO A 146 "
           pdb=" CA  PRO A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -85.03  -94.97     0      5.00e+00 4.00e-02 3.61e+02
  dihedral pdb=" CB  CYS E 391 "
           pdb=" SG  CYS E 391 "
           pdb=" SG  CYS E 525 "
           pdb=" CB  CYS E 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   17.56   75.44     1      1.00e+01 1.00e-02 7.19e+01
  dihedral pdb=" CA  CYS A 344 "
           pdb=" C   CYS A 344 "
           pdb=" N   HIS A 345 "
           pdb=" CA  HIS A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.20   26.80     0      5.00e+00 4.00e-02 2.87e+01
  ... (remaining 3902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 846
       0.099 -    0.198: 75
       0.198 -    0.297: 11
       0.297 -    0.395: 3
       0.395 -    0.494: 4
  Chirality restraints: 939
  Sorted by residual:
  chirality pdb=" CA  LYS A 353 "
            pdb=" N   LYS A 353 "
            pdb=" C   LYS A 353 "
            pdb=" CB  LYS A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.11e+00
  chirality pdb=" CA  PHE E 375 "
            pdb=" N   PHE E 375 "
            pdb=" C   PHE E 375 "
            pdb=" CB  PHE E 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.66e+00
  chirality pdb=" CA  ALA E 372 "
            pdb=" N   ALA E 372 "
            pdb=" C   ALA E 372 "
            pdb=" CB  ALA E 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.02    0.47 2.00e-01 2.50e+01 5.45e+00
  ... (remaining 936 not shown)

  Planarity restraints: 1166
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 368 "   -0.023 2.00e-02 2.50e+03   4.46e-02 1.99e+01
        pdb=" C   LEU E 368 "    0.077 2.00e-02 2.50e+03
        pdb=" O   LEU E 368 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   TYR E 369 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 500 "    0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   THR E 500 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   THR E 500 "    0.027 2.00e-02 2.50e+03
        pdb=" N   TYR E 501 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 367 "    0.019 2.00e-02 2.50e+03   3.69e-02 1.36e+01
        pdb=" C   VAL E 367 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   VAL E 367 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU E 368 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1163 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 2240
        2.84 -     3.36: 5639
        3.36 -     3.87: 10703
        3.87 -     4.39: 12421
        4.39 -     4.90: 20478
  Nonbonded interactions: 51481
  Sorted by model distance:
  nonbonded pdb=" O   THR A 449 "
            pdb=" OG1 THR A 453 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   SER A 254 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OD1 ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   ASN A 121 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OG1 THR E 500 "
            pdb=" OH  TYR A  41 "
     model   vdw
     2.371 3.040
  ... (remaining 51476 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
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   0.087   6618  Z= 0.477
  Angle     :  1.072  16.306   9000  Z= 0.648
  Chirality :  0.071   0.494    939
  Planarity :  0.007   0.062   1166
  Dihedral  : 15.403  94.965   2390
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  4.70 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  7.90 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.05 (0.22), residues: 787
  helix: -4.47 (0.12), residues: 325
  sheet: -2.25 (0.93), residues: 35
  loop : -2.50 (0.25), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 482 
 TYR   0.016   0.002   TYR A 183 
 PHE   0.020   0.002   PHE A  32 
 TRP   0.022   0.002   TRP A 478 
 HIS   0.018   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00785 ( 6611)
  covalent geometry    : angle       1.06763 ( 8986)
  SS BOND              : bond        0.01206 (    7)
  SS BOND              : angle       2.57311 (   14)
  hydrogen bonds       : bond        0.32339 (  200)
  hydrogen bonds       : angle       9.88967 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 250
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  358 ILE cc_start: 0.8796 (mt) cc_final: 0.8589 (mt)
REVERT: E  422 ASN cc_start: 0.8156 (m110) cc_final: 0.7908 (m110)
REVERT: E  442 ASP cc_start: 0.8719 (t70) cc_final: 0.8280 (t0)
REVERT: E  461 LEU cc_start: 0.8407 (mt) cc_final: 0.8180 (mp)
REVERT: E  467 ASP cc_start: 0.7953 (p0) cc_final: 0.7523 (p0)
REVERT: E  468 ILE cc_start: 0.9020 (pt) cc_final: 0.8803 (pt)
REVERT: E  471 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7784 (tp30)
REVERT: E  474 GLN cc_start: 0.7884 (tt0) cc_final: 0.7600 (tt0)
REVERT: E  492 LEU cc_start: 0.8677 (mt) cc_final: 0.8360 (mt)
REVERT: E  494 SER cc_start: 0.9040 (m) cc_final: 0.8690 (p)
REVERT: A   22 GLU cc_start: 0.7459 (tp30) cc_final: 0.7254 (tp30)
REVERT: A   26 LYS cc_start: 0.8012 (mttt) cc_final: 0.7757 (mmmm)
REVERT: A   47 SER cc_start: 0.8583 (t) cc_final: 0.8333 (t)
REVERT: A   55 THR cc_start: 0.7870 (m) cc_final: 0.7165 (p)
REVERT: A   64 ASN cc_start: 0.8703 (t0) cc_final: 0.8502 (t0)
REVERT: A  101 GLN cc_start: 0.8013 (tt0) cc_final: 0.7706 (mt0)
REVERT: A  144 LEU cc_start: 0.7666 (tp) cc_final: 0.7362 (tp)
REVERT: A  157 ASP cc_start: 0.7950 (m-30) cc_final: 0.7695 (t70)
REVERT: A  161 ARG cc_start: 0.8378 (mtp180) cc_final: 0.8063 (mmm-85)
REVERT: A  163 TRP cc_start: 0.7499 (t60) cc_final: 0.7196 (t60)
REVERT: A  168 TRP cc_start: 0.8242 (t-100) cc_final: 0.7758 (t-100)
REVERT: A  181 GLU cc_start: 0.7868 (tp30) cc_final: 0.7609 (tp30)
REVERT: A  186 LEU cc_start: 0.8592 (tp) cc_final: 0.8377 (tt)
REVERT: A  215 TYR cc_start: 0.8248 (m-80) cc_final: 0.7927 (m-80)
REVERT: A  219 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7514 (mtm-85)
REVERT: A  227 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7520 (mm-30)
REVERT: A  265 HIS cc_start: 0.8826 (p-80) cc_final: 0.7926 (p-80)
REVERT: A  267 LEU cc_start: 0.8603 (mp) cc_final: 0.8280 (mm)
REVERT: A  271 TRP cc_start: 0.4633 (t60) cc_final: 0.4300 (t60)
REVERT: A  277 ASN cc_start: 0.8575 (m-40) cc_final: 0.8282 (m-40)
REVERT: A  302 TRP cc_start: 0.8349 (m-10) cc_final: 0.7971 (m-10)
REVERT: A  310 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7629 (mm-30)
REVERT: A  313 LYS cc_start: 0.8259 (mttt) cc_final: 0.7521 (mtpt)
REVERT: A  323 MET cc_start: 0.8182 (mmm) cc_final: 0.7902 (mmm)
REVERT: A  332 MET cc_start: 0.7968 (ttp) cc_final: 0.7330 (tmm)
REVERT: A  341 LYS cc_start: 0.7902 (tptt) cc_final: 0.7604 (tptt)
REVERT: A  363 LYS cc_start: 0.8480 (mtmm) cc_final: 0.7947 (mppt)
REVERT: A  408 MET cc_start: 0.7901 (mmt) cc_final: 0.7490 (mmp)
REVERT: A  419 LYS cc_start: 0.8243 (tptp) cc_final: 0.8020 (mttt)
REVERT: A  423 LEU cc_start: 0.8754 (mt) cc_final: 0.8226 (mt)
REVERT: A  437 ASN cc_start: 0.7487 (m-40) cc_final: 0.7193 (m-40)
REVERT: A  459 TRP cc_start: 0.8262 (t60) cc_final: 0.7977 (t60)
REVERT: A  462 MET cc_start: 0.7529 (mtm) cc_final: 0.7268 (mtp)
REVERT: A  465 LYS cc_start: 0.8708 (mttt) cc_final: 0.8355 (ttmt)
REVERT: A  473 TRP cc_start: 0.7532 (t-100) cc_final: 0.6667 (t-100)
REVERT: A  475 LYS cc_start: 0.8865 (tppt) cc_final: 0.8637 (tptp)
REVERT: A  499 ASP cc_start: 0.7772 (m-30) cc_final: 0.6845 (t0)
REVERT: A  500 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.7813 (Cg_exo)
REVERT: A  534 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8341 (mmmm)
REVERT: A  579 MET cc_start: 0.8615 (ttp) cc_final: 0.8392 (ttm)
REVERT: A  582 ARG cc_start: 0.7412 (tpp80) cc_final: 0.6851 (tpp80)
REVERT: A  603 PHE cc_start: 0.7057 (t80) cc_final: 0.6646 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 252
  average time/residue: 0.0895
  time to fit residues: 28.3745
Evaluate side-chains
  227 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 224
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  483 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.0040
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
E 417 ASN
E 477 ASN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 ASN
A 121 ASN
A 330 ASN
A 373 HIS
A 417 HIS
A 540 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.112908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.097439 restraints weight = 11893.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100985 restraints weight = 5499.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.103239 restraints weight = 3107.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.104738 restraints weight = 2024.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.105574 restraints weight = 1463.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6618  Z= 0.172
  Angle     :  0.653   8.532   9000  Z= 0.339
  Chirality :  0.045   0.126    939
  Planarity :  0.005   0.035   1166
  Dihedral  :  5.444  65.876    864
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.38 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.61 (0.26), residues: 787
  helix: -3.18 (0.20), residues: 353
  sheet: -1.51 (0.90), residues: 34
  loop : -1.60 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 403 
 TYR   0.016   0.002   TYR E 473 
 PHE   0.013   0.001   PHE E 490 
 TRP   0.016   0.001   TRP A 478 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6611)
  covalent geometry    : angle       0.64984 ( 8986)
  SS BOND              : bond        0.00507 (    7)
  SS BOND              : angle       1.65400 (   14)
  hydrogen bonds       : bond        0.05105 (  200)
  hydrogen bonds       : angle       5.57485 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 226
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  422 ASN cc_start: 0.8111 (m110) cc_final: 0.7739 (m-40)
REVERT: E  442 ASP cc_start: 0.8747 (t70) cc_final: 0.8231 (t0)
REVERT: E  465 GLU cc_start: 0.7875 (tt0) cc_final: 0.7619 (tt0)
REVERT: E  467 ASP cc_start: 0.7721 (p0) cc_final: 0.7461 (p0)
REVERT: E  489 TYR cc_start: 0.7075 (m-80) cc_final: 0.6862 (m-80)
REVERT: E  494 SER cc_start: 0.8834 (m) cc_final: 0.8356 (p)
REVERT: A   22 GLU cc_start: 0.7257 (tp30) cc_final: 0.7011 (tp30)
REVERT: A   23 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7230 (mp0)
REVERT: A   26 LYS cc_start: 0.8184 (mttt) cc_final: 0.7930 (mmtt)
REVERT: A   40 PHE cc_start: 0.8644 (t80) cc_final: 0.8262 (t80)
REVERT: A   47 SER cc_start: 0.8716 (t) cc_final: 0.8419 (t)
REVERT: A   55 THR cc_start: 0.7789 (m) cc_final: 0.7116 (p)
REVERT: A   62 MET cc_start: 0.8049 (tmm) cc_final: 0.7262 (tmm)
REVERT: A  101 GLN cc_start: 0.7932 (tt0) cc_final: 0.7677 (mt0)
REVERT: A  102 GLN cc_start: 0.8072 (pp30) cc_final: 0.7823 (pp30)
REVERT: A  105 SER cc_start: 0.8383 (p) cc_final: 0.7971 (t)
REVERT: A  126 ILE cc_start: 0.8947 (tp) cc_final: 0.8633 (tt)
REVERT: A  142 LEU cc_start: 0.7752 (mt) cc_final: 0.7549 (mt)
REVERT: A  144 LEU cc_start: 0.8256 (tp) cc_final: 0.7765 (tp)
REVERT: A  158 TYR cc_start: 0.7303 (t80) cc_final: 0.6814 (t80)
REVERT: A  161 ARG cc_start: 0.8636 (mtp180) cc_final: 0.7883 (ttp-170)
REVERT: A  168 TRP cc_start: 0.8302 (t-100) cc_final: 0.7891 (t-100)
REVERT: A  182 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: A  186 LEU cc_start: 0.8502 (tp) cc_final: 0.8158 (tp)
REVERT: A  209 VAL cc_start: 0.8696 (t) cc_final: 0.8462 (m)
REVERT: A  219 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7827 (mtm-85)
REVERT: A  227 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7752 (tp30)
REVERT: A  265 HIS cc_start: 0.8966 (p-80) cc_final: 0.8260 (p-80)
REVERT: A  267 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8385 (mm)
REVERT: A  271 TRP cc_start: 0.4915 (t60) cc_final: 0.4340 (t60)
REVERT: A  299 ASP cc_start: 0.8001 (t0) cc_final: 0.7782 (t0)
REVERT: A  310 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7651 (mm-30)
REVERT: A  313 LYS cc_start: 0.8233 (mttt) cc_final: 0.7694 (mtpt)
REVERT: A  325 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7303 (tp-100)
REVERT: A  332 MET cc_start: 0.7965 (ttp) cc_final: 0.7533 (tmm)
REVERT: A  353 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8069 (mmmt)
REVERT: A  368 ASP cc_start: 0.8092 (t0) cc_final: 0.7235 (t0)
REVERT: A  375 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7804 (mm-30)
REVERT: A  429 GLN cc_start: 0.7398 (tp40) cc_final: 0.7118 (tp40)
REVERT: A  462 MET cc_start: 0.7537 (mtm) cc_final: 0.7313 (mtp)
REVERT: A  465 LYS cc_start: 0.8717 (mttt) cc_final: 0.8350 (ttmt)
REVERT: A  472 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7472 (mm-40)
REVERT: A  475 LYS cc_start: 0.8348 (tppt) cc_final: 0.8099 (tmtt)
REVERT: A  476 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7719 (mtpt)
REVERT: A  499 ASP cc_start: 0.8237 (m-30) cc_final: 0.7861 (t0)
REVERT: A  504 PHE cc_start: 0.7939 (t80) cc_final: 0.7657 (t80)
REVERT: A  574 VAL cc_start: 0.9004 (m) cc_final: 0.8770 (p)
REVERT: A  582 ARG cc_start: 0.7453 (tpp80) cc_final: 0.7015 (mpp80)
REVERT: A  589 GLU cc_start: 0.7841 (tp30) cc_final: 0.7612 (tp30)
REVERT: A  598 GLN cc_start: 0.8358 (tt0) cc_final: 0.8116 (mt0)
REVERT: A  603 PHE cc_start: 0.6969 (t80) cc_final: 0.6612 (t80)
  outliers start: 20
  outliers final: 6
  residues processed: 239
  average time/residue: 0.0904
  time to fit residues: 27.4709
Evaluate side-chains
  226 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 218
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.111995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.096734 restraints weight = 11887.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.100246 restraints weight = 5511.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.102504 restraints weight = 3123.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.103990 restraints weight = 2035.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.104996 restraints weight = 1474.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6618  Z= 0.166
  Angle     :  0.647   9.285   9000  Z= 0.328
  Chirality :  0.045   0.129    939
  Planarity :  0.004   0.042   1166
  Dihedral  :  5.053  58.312    862
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.67 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.41 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.74 (0.28), residues: 787
  helix: -2.40 (0.23), residues: 354
  sheet: -1.28 (0.89), residues: 34
  loop : -1.17 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 357 
 TYR   0.017   0.001   TYR A 215 
 PHE   0.028   0.002   PHE A 428 
 TRP   0.016   0.001   TRP E 436 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6611)
  covalent geometry    : angle       0.64364 ( 8986)
  SS BOND              : bond        0.00571 (    7)
  SS BOND              : angle       1.72634 (   14)
  hydrogen bonds       : bond        0.04585 (  200)
  hydrogen bonds       : angle       4.84737 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 231
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: E  335 LEU cc_start: 0.8474 (tp) cc_final: 0.8231 (tp)
REVERT: E  403 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7608 (ptm-80)
REVERT: E  442 ASP cc_start: 0.8695 (t70) cc_final: 0.8210 (t0)
REVERT: E  467 ASP cc_start: 0.7755 (p0) cc_final: 0.7433 (p0)
REVERT: E  473 TYR cc_start: 0.7707 (t80) cc_final: 0.7311 (t80)
REVERT: E  494 SER cc_start: 0.8814 (m) cc_final: 0.8326 (p)
REVERT: E  505 HIS cc_start: 0.8451 (m170) cc_final: 0.8180 (m170)
REVERT: A   22 GLU cc_start: 0.7297 (tp30) cc_final: 0.7086 (tp30)
REVERT: A   23 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7290 (mt-10)
REVERT: A   26 LYS cc_start: 0.8216 (mttt) cc_final: 0.7917 (mmtt)
REVERT: A   40 PHE cc_start: 0.8706 (t80) cc_final: 0.8356 (t80)
REVERT: A   47 SER cc_start: 0.8789 (t) cc_final: 0.8487 (t)
REVERT: A   55 THR cc_start: 0.7749 (m) cc_final: 0.7123 (p)
REVERT: A   62 MET cc_start: 0.8108 (tmm) cc_final: 0.7259 (tmm)
REVERT: A  101 GLN cc_start: 0.7872 (tt0) cc_final: 0.7666 (mt0)
REVERT: A  102 GLN cc_start: 0.8252 (pp30) cc_final: 0.7724 (pp30)
REVERT: A  105 SER cc_start: 0.8413 (p) cc_final: 0.8051 (t)
REVERT: A  110 GLU cc_start: 0.6962 (tp30) cc_final: 0.6738 (tp30)
REVERT: A  126 ILE cc_start: 0.8972 (tp) cc_final: 0.8670 (tt)
REVERT: A  144 LEU cc_start: 0.8410 (tp) cc_final: 0.7844 (tp)
REVERT: A  160 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6947 (tm-30)
REVERT: A  161 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8163 (ttp-170)
REVERT: A  166 GLU cc_start: 0.7345 (tp30) cc_final: 0.6802 (tp30)
REVERT: A  168 TRP cc_start: 0.8255 (t-100) cc_final: 0.7778 (t-100)
REVERT: A  182 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6759 (tm-30)
REVERT: A  186 LEU cc_start: 0.8419 (tp) cc_final: 0.8055 (tp)
REVERT: A  245 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8183 (mtp-110)
REVERT: A  271 TRP cc_start: 0.4877 (t60) cc_final: 0.4255 (t60)
REVERT: A  273 ARG cc_start: 0.8538 (ttt90) cc_final: 0.8289 (ttt90)
REVERT: A  299 ASP cc_start: 0.8006 (t0) cc_final: 0.7726 (t0)
REVERT: A  313 LYS cc_start: 0.8048 (mttt) cc_final: 0.7707 (mtpt)
REVERT: A  320 LEU cc_start: 0.8932 (mm) cc_final: 0.8730 (mt)
REVERT: A  323 MET cc_start: 0.8329 (mmt) cc_final: 0.8048 (mmt)
REVERT: A  325 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7454 (tp-100)
REVERT: A  332 MET cc_start: 0.7883 (ttp) cc_final: 0.7582 (tmm)
REVERT: A  353 LYS cc_start: 0.8312 (mtpt) cc_final: 0.8009 (mtpt)
REVERT: A  363 LYS cc_start: 0.8798 (mppt) cc_final: 0.8458 (mppt)
REVERT: A  369 PHE cc_start: 0.8848 (t80) cc_final: 0.8471 (t80)
REVERT: A  375 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7749 (mm-30)
REVERT: A  380 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8353 (mm110)
REVERT: A  388 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7999 (mm-40)
REVERT: A  406 GLU cc_start: 0.7859 (tp30) cc_final: 0.7577 (tp30)
REVERT: A  429 GLN cc_start: 0.7374 (tp40) cc_final: 0.7132 (tp40)
REVERT: A  465 LYS cc_start: 0.8819 (mttt) cc_final: 0.8362 (ttmt)
REVERT: A  470 LYS cc_start: 0.7175 (tppt) cc_final: 0.6907 (tppt)
REVERT: A  475 LYS cc_start: 0.8472 (tppt) cc_final: 0.8182 (tmtt)
REVERT: A  476 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7858 (mtpt)
REVERT: A  504 PHE cc_start: 0.8084 (t80) cc_final: 0.7749 (t80)
REVERT: A  514 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7906 (mtm110)
REVERT: A  559 ARG cc_start: 0.8111 (ptt180) cc_final: 0.7838 (ptm160)
REVERT: A  574 VAL cc_start: 0.8988 (m) cc_final: 0.8773 (p)
REVERT: A  598 GLN cc_start: 0.8376 (tt0) cc_final: 0.8160 (mt0)
REVERT: A  603 PHE cc_start: 0.7044 (t80) cc_final: 0.6691 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 237
  average time/residue: 0.0935
  time to fit residues: 27.7280
Evaluate side-chains
  219 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 208
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0470
   chunk 76 optimal weight:    0.0770
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 194 ASN
A 540 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.095778 restraints weight = 12147.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.099374 restraints weight = 5633.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.101672 restraints weight = 3189.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.103195 restraints weight = 2075.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.104201 restraints weight = 1500.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6618  Z= 0.157
  Angle     :  0.633   9.983   9000  Z= 0.321
  Chirality :  0.045   0.139    939
  Planarity :  0.004   0.031   1166
  Dihedral  :  4.899  54.359    862
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.54 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.41 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.29), residues: 787
  helix: -1.97 (0.24), residues: 365
  sheet: -1.41 (0.84), residues: 36
  loop : -0.90 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 357 
 TYR   0.015   0.001   TYR A 180 
 PHE   0.016   0.001   PHE A 400 
 TRP   0.015   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6611)
  covalent geometry    : angle       0.63015 ( 8986)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       1.76275 (   14)
  hydrogen bonds       : bond        0.04160 (  200)
  hydrogen bonds       : angle       4.58942 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 215
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: E  335 LEU cc_start: 0.8467 (tp) cc_final: 0.8204 (tp)
REVERT: E  347 PHE cc_start: 0.8839 (m-10) cc_final: 0.8492 (m-80)
REVERT: E  357 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7768 (mtp85)
REVERT: E  403 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7439 (ptm-80)
REVERT: E  422 ASN cc_start: 0.8252 (m110) cc_final: 0.7902 (m110)
REVERT: E  442 ASP cc_start: 0.8736 (t70) cc_final: 0.8289 (t0)
REVERT: E  473 TYR cc_start: 0.7773 (t80) cc_final: 0.7443 (t80)
REVERT: E  494 SER cc_start: 0.8803 (m) cc_final: 0.8289 (p)
REVERT: E  505 HIS cc_start: 0.8330 (m170) cc_final: 0.8001 (m170)
REVERT: E  517 LEU cc_start: 0.8653 (mm) cc_final: 0.8231 (mp)
REVERT: A   22 GLU cc_start: 0.7326 (tp30) cc_final: 0.7116 (tp30)
REVERT: A   23 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7163 (mp0)
REVERT: A   26 LYS cc_start: 0.8230 (mttt) cc_final: 0.7947 (mmtt)
REVERT: A   40 PHE cc_start: 0.8651 (t80) cc_final: 0.8320 (t80)
REVERT: A   47 SER cc_start: 0.8796 (t) cc_final: 0.8371 (p)
REVERT: A   55 THR cc_start: 0.7737 (m) cc_final: 0.7133 (p)
REVERT: A   62 MET cc_start: 0.8176 (tmm) cc_final: 0.7315 (tmm)
REVERT: A  101 GLN cc_start: 0.7869 (tt0) cc_final: 0.7321 (tp40)
REVERT: A  102 GLN cc_start: 0.8372 (pp30) cc_final: 0.8031 (pp30)
REVERT: A  105 SER cc_start: 0.8315 (p) cc_final: 0.7973 (t)
REVERT: A  110 GLU cc_start: 0.7098 (tp30) cc_final: 0.6797 (tp30)
REVERT: A  121 ASN cc_start: 0.8510 (m-40) cc_final: 0.8308 (m-40)
REVERT: A  123 MET cc_start: 0.8119 (ttt) cc_final: 0.7742 (mtt)
REVERT: A  144 LEU cc_start: 0.8428 (tp) cc_final: 0.7770 (tp)
REVERT: A  166 GLU cc_start: 0.7459 (tp30) cc_final: 0.7238 (tp30)
REVERT: A  168 TRP cc_start: 0.8303 (t-100) cc_final: 0.7771 (t-100)
REVERT: A  182 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: A  186 LEU cc_start: 0.8440 (tp) cc_final: 0.8168 (tp)
REVERT: A  204 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8259 (mtm180)
REVERT: A  209 VAL cc_start: 0.8735 (t) cc_final: 0.8515 (m)
REVERT: A  227 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7624 (tp30)
REVERT: A  249 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6822 (tmm)
REVERT: A  267 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8294 (mm)
REVERT: A  271 TRP cc_start: 0.4995 (t60) cc_final: 0.4182 (t60)
REVERT: A  273 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8293 (ttt90)
REVERT: A  299 ASP cc_start: 0.8134 (t0) cc_final: 0.7816 (t0)
REVERT: A  313 LYS cc_start: 0.8000 (mttt) cc_final: 0.7734 (mtpt)
REVERT: A  323 MET cc_start: 0.8262 (mmt) cc_final: 0.8054 (mmt)
REVERT: A  332 MET cc_start: 0.7837 (ttp) cc_final: 0.7558 (tmm)
REVERT: A  353 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8069 (mtpt)
REVERT: A  375 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7678 (mm-30)
REVERT: A  406 GLU cc_start: 0.7945 (tp30) cc_final: 0.7663 (tp30)
REVERT: A  419 LYS cc_start: 0.8223 (tptp) cc_final: 0.8000 (mtpt)
REVERT: A  429 GLN cc_start: 0.7395 (tp40) cc_final: 0.6868 (tp40)
REVERT: A  465 LYS cc_start: 0.8825 (mttt) cc_final: 0.8334 (ttmt)
REVERT: A  472 GLN cc_start: 0.7759 (mm110) cc_final: 0.7526 (mm-40)
REVERT: A  473 TRP cc_start: 0.7516 (t-100) cc_final: 0.6587 (t-100)
REVERT: A  475 LYS cc_start: 0.8316 (tppt) cc_final: 0.8091 (tmtt)
REVERT: A  480 MET cc_start: 0.8707 (mmm) cc_final: 0.8421 (tpp)
REVERT: A  483 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6995 (tm-30)
REVERT: A  484 ILE cc_start: 0.8711 (mt) cc_final: 0.8284 (mm)
REVERT: A  504 PHE cc_start: 0.8089 (t80) cc_final: 0.7630 (t80)
REVERT: A  557 MET cc_start: 0.7969 (tmm) cc_final: 0.7674 (tmm)
REVERT: A  559 ARG cc_start: 0.8174 (ptt180) cc_final: 0.7892 (ptm160)
REVERT: A  574 VAL cc_start: 0.8999 (m) cc_final: 0.8762 (p)
REVERT: A  582 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7083 (tpp80)
REVERT: A  603 PHE cc_start: 0.7149 (t80) cc_final: 0.6768 (t80)
  outliers start: 21
  outliers final: 11
  residues processed: 226
  average time/residue: 0.0980
  time to fit residues: 27.5854
Evaluate side-chains
  218 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 204
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.1980
   chunk 46 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  61 ASN
A  64 ASN
A 239 HIS
** A 540 HIS ** 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 = 0.3434 r_free = 0.3434 target = 0.108107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.092759 restraints weight = 12368.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.096286 restraints weight = 5780.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.098492 restraints weight = 3287.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.099991 restraints weight = 2164.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.100820 restraints weight = 1568.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6618  Z= 0.265
  Angle     :  0.733   9.631   9000  Z= 0.370
  Chirality :  0.050   0.155    939
  Planarity :  0.004   0.042   1166
  Dihedral  :  5.284  52.998    862
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.99 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.29), residues: 787
  helix: -1.77 (0.25), residues: 365
  sheet: -1.41 (0.83), residues: 36
  loop : -0.81 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 245 
 TYR   0.017   0.002   TYR A 158 
 PHE   0.019   0.002   PHE A 400 
 TRP   0.017   0.002   TRP E 436 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 6611)
  covalent geometry    : angle       0.72720 ( 8986)
  SS BOND              : bond        0.00382 (    7)
  SS BOND              : angle       2.41064 (   14)
  hydrogen bonds       : bond        0.04599 (  200)
  hydrogen bonds       : angle       4.83472 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 220
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7717 (mtp85)
REVERT: E  380 TYR cc_start: 0.8974 (m-80) cc_final: 0.8701 (m-80)
REVERT: E  403 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7620 (ptm-80)
REVERT: E  422 ASN cc_start: 0.8258 (m110) cc_final: 0.7844 (m-40)
REVERT: E  442 ASP cc_start: 0.8674 (t70) cc_final: 0.8123 (t0)
REVERT: E  494 SER cc_start: 0.8904 (m) cc_final: 0.8385 (p)
REVERT: E  495 TYR cc_start: 0.8543 (m-10) cc_final: 0.8316 (m-80)
REVERT: E  505 HIS cc_start: 0.8399 (m170) cc_final: 0.8198 (m170)
REVERT: A   22 GLU cc_start: 0.7389 (tp30) cc_final: 0.7181 (tp30)
REVERT: A   23 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7180 (mp0)
REVERT: A   26 LYS cc_start: 0.8263 (mttt) cc_final: 0.7923 (mmtt)
REVERT: A   31 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7154 (tttp)
REVERT: A   47 SER cc_start: 0.8787 (t) cc_final: 0.8428 (p)
REVERT: A   55 THR cc_start: 0.7898 (m) cc_final: 0.7328 (p)
REVERT: A   62 MET cc_start: 0.8243 (tmm) cc_final: 0.7338 (tmm)
REVERT: A   88 ILE cc_start: 0.8856 (mt) cc_final: 0.8594 (mm)
REVERT: A  101 GLN cc_start: 0.7925 (tt0) cc_final: 0.7590 (tt0)
REVERT: A  102 GLN cc_start: 0.8571 (pp30) cc_final: 0.8275 (pp30)
REVERT: A  110 GLU cc_start: 0.7061 (tp30) cc_final: 0.6719 (tp30)
REVERT: A  121 ASN cc_start: 0.8714 (m-40) cc_final: 0.8426 (m-40)
REVERT: A  144 LEU cc_start: 0.8354 (tp) cc_final: 0.7987 (tp)
REVERT: A  161 ARG cc_start: 0.8833 (mtp85) cc_final: 0.8304 (ttp-170)
REVERT: A  168 TRP cc_start: 0.8410 (t-100) cc_final: 0.7899 (t-100)
REVERT: A  182 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6924 (tm-30)
REVERT: A  186 LEU cc_start: 0.8421 (tp) cc_final: 0.8068 (tp)
REVERT: A  204 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8159 (mtm180)
REVERT: A  209 VAL cc_start: 0.8749 (t) cc_final: 0.8443 (m)
REVERT: A  227 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7648 (tp30)
REVERT: A  249 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7140 (tmm)
REVERT: A  271 TRP cc_start: 0.4966 (t60) cc_final: 0.3910 (t60)
REVERT: A  273 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8320 (ttt90)
REVERT: A  299 ASP cc_start: 0.8237 (t0) cc_final: 0.7959 (t0)
REVERT: A  313 LYS cc_start: 0.8132 (mttt) cc_final: 0.7892 (mtpt)
REVERT: A  328 TRP cc_start: 0.8643 (m100) cc_final: 0.8321 (m100)
REVERT: A  353 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8149 (mtpt)
REVERT: A  375 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7712 (mm-30)
REVERT: A  406 GLU cc_start: 0.7971 (tp30) cc_final: 0.7739 (tp30)
REVERT: A  419 LYS cc_start: 0.8134 (tptp) cc_final: 0.7931 (mtpt)
REVERT: A  429 GLN cc_start: 0.7426 (tp40) cc_final: 0.6814 (tp40)
REVERT: A  465 LYS cc_start: 0.8838 (mttt) cc_final: 0.8322 (ttmt)
REVERT: A  473 TRP cc_start: 0.7507 (t-100) cc_final: 0.6690 (t-100)
REVERT: A  475 LYS cc_start: 0.8484 (tppt) cc_final: 0.8254 (tmtt)
REVERT: A  476 LYS cc_start: 0.8242 (mtpt) cc_final: 0.8026 (mtpt)
REVERT: A  480 MET cc_start: 0.8718 (mmm) cc_final: 0.8461 (tpp)
REVERT: A  484 ILE cc_start: 0.8708 (mt) cc_final: 0.8445 (mt)
REVERT: A  499 ASP cc_start: 0.8520 (m-30) cc_final: 0.8315 (t0)
REVERT: A  518 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7689 (tmm-80)
REVERT: A  557 MET cc_start: 0.7971 (tmm) cc_final: 0.7652 (tmm)
REVERT: A  559 ARG cc_start: 0.8255 (ptt180) cc_final: 0.7944 (ptm160)
REVERT: A  564 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7485 (mm-30)
REVERT: A  574 VAL cc_start: 0.9017 (m) cc_final: 0.8773 (p)
REVERT: A  582 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7134 (tpp80)
REVERT: A  603 PHE cc_start: 0.7203 (t80) cc_final: 0.6857 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 227
  average time/residue: 0.0946
  time to fit residues: 26.7232
Evaluate side-chains
  234 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 214
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  503 VAL
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0970
   chunk 48 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 73 optimal weight:    0.2980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 HIS
A 508 ASN
A 540 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.110917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.095507 restraints weight = 12316.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.099084 restraints weight = 5724.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.101391 restraints weight = 3239.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.102899 restraints weight = 2099.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.103854 restraints weight = 1512.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6618  Z= 0.157
  Angle     :  0.667   7.803   9000  Z= 0.333
  Chirality :  0.045   0.126    939
  Planarity :  0.004   0.043   1166
  Dihedral  :  5.059  52.346    862
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.54 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 27.30 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.29), residues: 787
  helix: -1.34 (0.25), residues: 371
  sheet: -1.39 (0.82), residues: 35
  loop : -0.64 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 219 
 TYR   0.015   0.001   TYR A 158 
 PHE   0.014   0.002   PHE A 400 
 TRP   0.016   0.001   TRP A 566 
 HIS   0.006   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6611)
  covalent geometry    : angle       0.66144 ( 8986)
  SS BOND              : bond        0.00349 (    7)
  SS BOND              : angle       2.22589 (   14)
  hydrogen bonds       : bond        0.04028 (  200)
  hydrogen bonds       : angle       4.58540 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7779 (ttp80)
REVERT: E  422 ASN cc_start: 0.8221 (m110) cc_final: 0.7903 (m-40)
REVERT: E  442 ASP cc_start: 0.8694 (t70) cc_final: 0.8072 (t0)
REVERT: E  494 SER cc_start: 0.8823 (m) cc_final: 0.8339 (p)
REVERT: A   23 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7193 (mp0)
REVERT: A   40 PHE cc_start: 0.8612 (t80) cc_final: 0.8299 (t80)
REVERT: A   47 SER cc_start: 0.8788 (t) cc_final: 0.8376 (p)
REVERT: A   55 THR cc_start: 0.7873 (m) cc_final: 0.7312 (p)
REVERT: A   62 MET cc_start: 0.8243 (tmm) cc_final: 0.7372 (tmm)
REVERT: A   81 GLN cc_start: 0.8155 (tp40) cc_final: 0.7884 (tp40)
REVERT: A  101 GLN cc_start: 0.7886 (tt0) cc_final: 0.7571 (tp40)
REVERT: A  102 GLN cc_start: 0.8591 (pp30) cc_final: 0.8342 (pp30)
REVERT: A  121 ASN cc_start: 0.8762 (m-40) cc_final: 0.8453 (m110)
REVERT: A  123 MET cc_start: 0.8329 (ttt) cc_final: 0.8071 (ttp)
REVERT: A  168 TRP cc_start: 0.8370 (t-100) cc_final: 0.7894 (t-100)
REVERT: A  182 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6729 (tm-30)
REVERT: A  186 LEU cc_start: 0.8406 (tp) cc_final: 0.8076 (tp)
REVERT: A  204 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.7917 (mtm-85)
REVERT: A  227 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7626 (tp30)
REVERT: A  249 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7074 (tmm)
REVERT: A  271 TRP cc_start: 0.5031 (t60) cc_final: 0.4040 (t60)
REVERT: A  273 ARG cc_start: 0.8441 (ttt90) cc_final: 0.8181 (ttt90)
REVERT: A  299 ASP cc_start: 0.8207 (t0) cc_final: 0.7953 (t0)
REVERT: A  307 ILE cc_start: 0.8510 (tp) cc_final: 0.8243 (tt)
REVERT: A  310 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7615 (mm-30)
REVERT: A  313 LYS cc_start: 0.8070 (mttt) cc_final: 0.7779 (mtpt)
REVERT: A  332 MET cc_start: 0.7746 (tmm) cc_final: 0.7487 (tmm)
REVERT: A  353 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8122 (mtpt)
REVERT: A  375 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7643 (mm-30)
REVERT: A  406 GLU cc_start: 0.7928 (tp30) cc_final: 0.7662 (tp30)
REVERT: A  465 LYS cc_start: 0.8800 (mttt) cc_final: 0.8309 (ttmt)
REVERT: A  473 TRP cc_start: 0.7632 (t-100) cc_final: 0.6714 (t-100)
REVERT: A  475 LYS cc_start: 0.8350 (tppt) cc_final: 0.8119 (tmtt)
REVERT: A  476 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7860 (mtpt)
REVERT: A  480 MET cc_start: 0.8625 (mmm) cc_final: 0.8313 (tpp)
REVERT: A  483 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6930 (tm-30)
REVERT: A  484 ILE cc_start: 0.8693 (mt) cc_final: 0.8266 (mm)
REVERT: A  499 ASP cc_start: 0.8453 (m-30) cc_final: 0.8248 (t0)
REVERT: A  518 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7614 (tmm-80)
REVERT: A  557 MET cc_start: 0.7878 (tmm) cc_final: 0.7575 (tmm)
REVERT: A  559 ARG cc_start: 0.8203 (ptt180) cc_final: 0.7925 (ptm160)
REVERT: A  564 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: A  574 VAL cc_start: 0.9021 (m) cc_final: 0.8756 (p)
REVERT: A  582 ARG cc_start: 0.7541 (tpp80) cc_final: 0.7076 (tpp80)
REVERT: A  598 GLN cc_start: 0.8421 (tt0) cc_final: 0.8140 (tm-30)
REVERT: A  603 PHE cc_start: 0.7201 (t80) cc_final: 0.6837 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 223
  average time/residue: 0.0941
  time to fit residues: 26.1293
Evaluate side-chains
  224 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  359 SER
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  472 ILE
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  608 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 62 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.108980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.093790 restraints weight = 12247.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.097265 restraints weight = 5708.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.099480 restraints weight = 3263.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.100953 restraints weight = 2126.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.101851 restraints weight = 1545.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6618  Z= 0.214
  Angle     :  0.715   9.922   9000  Z= 0.356
  Chirality :  0.048   0.158    939
  Planarity :  0.004   0.042   1166
  Dihedral  :  5.138  51.270    861
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 26.58 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.30), residues: 787
  helix: -1.17 (0.26), residues: 374
  sheet: -1.36 (0.79), residues: 35
  loop : -0.55 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 357 
 TYR   0.020   0.002   TYR A 180 
 PHE   0.031   0.002   PHE A 428 
 TRP   0.019   0.002   TRP A 566 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 6611)
  covalent geometry    : angle       0.70790 ( 8986)
  SS BOND              : bond        0.00369 (    7)
  SS BOND              : angle       2.60768 (   14)
  hydrogen bonds       : bond        0.04298 (  200)
  hydrogen bonds       : angle       4.60106 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 208
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7942 (ttp80)
REVERT: E  422 ASN cc_start: 0.8243 (m110) cc_final: 0.7921 (m-40)
REVERT: E  442 ASP cc_start: 0.8656 (t70) cc_final: 0.8110 (t0)
REVERT: E  494 SER cc_start: 0.8830 (m) cc_final: 0.8323 (p)
REVERT: E  505 HIS cc_start: 0.8368 (m170) cc_final: 0.7982 (m170)
REVERT: A   23 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7199 (mp0)
REVERT: A   26 LYS cc_start: 0.8302 (mttt) cc_final: 0.7960 (mmtt)
REVERT: A   31 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7254 (tttp)
REVERT: A   40 PHE cc_start: 0.8641 (t80) cc_final: 0.8402 (t80)
REVERT: A   47 SER cc_start: 0.8795 (t) cc_final: 0.8419 (p)
REVERT: A   55 THR cc_start: 0.7972 (m) cc_final: 0.7426 (p)
REVERT: A   62 MET cc_start: 0.8297 (tmm) cc_final: 0.7414 (tmm)
REVERT: A   81 GLN cc_start: 0.8196 (tp40) cc_final: 0.7924 (tp40)
REVERT: A  101 GLN cc_start: 0.7873 (tt0) cc_final: 0.7586 (tp40)
REVERT: A  121 ASN cc_start: 0.8854 (m-40) cc_final: 0.8555 (m-40)
REVERT: A  123 MET cc_start: 0.8322 (ttt) cc_final: 0.8085 (ttp)
REVERT: A  157 ASP cc_start: 0.7219 (t0) cc_final: 0.6901 (t0)
REVERT: A  163 TRP cc_start: 0.7786 (t60) cc_final: 0.7455 (t60)
REVERT: A  168 TRP cc_start: 0.8405 (t-100) cc_final: 0.7928 (t-100)
REVERT: A  186 LEU cc_start: 0.8396 (tp) cc_final: 0.8137 (tp)
REVERT: A  204 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.7885 (mtm-85)
REVERT: A  227 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7636 (tp30)
REVERT: A  249 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7222 (tmm)
REVERT: A  271 TRP cc_start: 0.4960 (t60) cc_final: 0.3868 (t60)
REVERT: A  273 ARG cc_start: 0.8531 (ttt90) cc_final: 0.8257 (ttt90)
REVERT: A  299 ASP cc_start: 0.8232 (t0) cc_final: 0.7988 (t0)
REVERT: A  307 ILE cc_start: 0.8501 (tp) cc_final: 0.8231 (tt)
REVERT: A  310 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7432 (mm-30)
REVERT: A  313 LYS cc_start: 0.7970 (mttt) cc_final: 0.7657 (mtpt)
REVERT: A  353 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8090 (mtpt)
REVERT: A  380 GLN cc_start: 0.8263 (mt0) cc_final: 0.7995 (mt0)
REVERT: A  465 LYS cc_start: 0.8835 (mttt) cc_final: 0.8280 (ttmt)
REVERT: A  473 TRP cc_start: 0.7408 (t-100) cc_final: 0.6534 (t-100)
REVERT: A  480 MET cc_start: 0.8648 (mmm) cc_final: 0.8373 (tpp)
REVERT: A  483 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6766 (tm-30)
REVERT: A  484 ILE cc_start: 0.8675 (mt) cc_final: 0.8184 (mm)
REVERT: A  518 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7648 (tmm-80)
REVERT: A  557 MET cc_start: 0.7772 (tmm) cc_final: 0.7501 (tmm)
REVERT: A  559 ARG cc_start: 0.8252 (ptt180) cc_final: 0.7998 (ptm160)
REVERT: A  574 VAL cc_start: 0.9018 (m) cc_final: 0.8746 (p)
REVERT: A  582 ARG cc_start: 0.7544 (tpp80) cc_final: 0.7118 (tpp80)
REVERT: A  598 GLN cc_start: 0.8306 (tt0) cc_final: 0.8091 (tm-30)
REVERT: A  603 PHE cc_start: 0.7239 (t80) cc_final: 0.6898 (t80)
  outliers start: 28
  outliers final: 23
  residues processed: 220
  average time/residue: 0.0942
  time to fit residues: 25.7646
Evaluate side-chains
  229 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  428 ASP
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  608 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0000
   overall best weight:    0.2184

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
E 394 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 ASN
A 134 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.111429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.095916 restraints weight = 12112.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099581 restraints weight = 5650.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.101977 restraints weight = 3214.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103403 restraints weight = 2085.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.104485 restraints weight = 1533.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6618  Z= 0.130
  Angle     :  0.674   8.809   9000  Z= 0.333
  Chirality :  0.045   0.144    939
  Planarity :  0.004   0.044   1166
  Dihedral  :  4.862  48.824    861
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 27.87 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.30), residues: 787
  helix: -0.83 (0.26), residues: 377
  sheet: -1.96 (0.67), residues: 47
  loop : -0.34 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.015   0.001   PHE A  32 
 TRP   0.013   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6611)
  covalent geometry    : angle       0.67020 ( 8986)
  SS BOND              : bond        0.00344 (    7)
  SS BOND              : angle       1.95424 (   14)
  hydrogen bonds       : bond        0.03798 (  200)
  hydrogen bonds       : angle       4.32197 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 210
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8348 (ttp80) cc_final: 0.8052 (ttp80)
REVERT: E  422 ASN cc_start: 0.8236 (m110) cc_final: 0.7888 (m-40)
REVERT: E  442 ASP cc_start: 0.8666 (t70) cc_final: 0.8106 (t0)
REVERT: E  494 SER cc_start: 0.8735 (m) cc_final: 0.8249 (p)
REVERT: E  505 HIS cc_start: 0.8283 (m170) cc_final: 0.7911 (m170)
REVERT: A   23 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7364 (mt-10)
REVERT: A   26 LYS cc_start: 0.8279 (mttt) cc_final: 0.7963 (mmtt)
REVERT: A   31 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7100 (tttp)
REVERT: A   40 PHE cc_start: 0.8566 (t80) cc_final: 0.8248 (t80)
REVERT: A   47 SER cc_start: 0.8792 (t) cc_final: 0.8385 (p)
REVERT: A   55 THR cc_start: 0.7931 (m) cc_final: 0.7379 (p)
REVERT: A   58 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8269 (t0)
REVERT: A   62 MET cc_start: 0.8270 (tmm) cc_final: 0.7366 (tmm)
REVERT: A   82 MET cc_start: 0.7729 (tpp) cc_final: 0.7509 (tpt)
REVERT: A  101 GLN cc_start: 0.7877 (tt0) cc_final: 0.7414 (tp40)
REVERT: A  121 ASN cc_start: 0.8863 (m-40) cc_final: 0.8535 (m110)
REVERT: A  123 MET cc_start: 0.8418 (ttt) cc_final: 0.8175 (ttp)
REVERT: A  168 TRP cc_start: 0.8377 (t-100) cc_final: 0.7774 (t-100)
REVERT: A  177 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6597 (tpt-90)
REVERT: A  186 LEU cc_start: 0.8364 (tp) cc_final: 0.8126 (tp)
REVERT: A  204 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.7810 (mtm-85)
REVERT: A  227 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7601 (tp30)
REVERT: A  249 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7178 (tmm)
REVERT: A  271 TRP cc_start: 0.5018 (t60) cc_final: 0.3995 (t60)
REVERT: A  273 ARG cc_start: 0.8422 (ttt90) cc_final: 0.8163 (ttt90)
REVERT: A  299 ASP cc_start: 0.8262 (t0) cc_final: 0.7992 (t0)
REVERT: A  307 ILE cc_start: 0.8436 (tp) cc_final: 0.8210 (tt)
REVERT: A  312 GLU cc_start: 0.7360 (tp30) cc_final: 0.6981 (tp30)
REVERT: A  353 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7963 (mmmt)
REVERT: A  375 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7443 (mm-30)
REVERT: A  376 MET cc_start: 0.8397 (ttp) cc_final: 0.8152 (ttp)
REVERT: A  441 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8052 (mmmt)
REVERT: A  465 LYS cc_start: 0.8750 (mttt) cc_final: 0.8201 (ttmt)
REVERT: A  473 TRP cc_start: 0.7569 (t-100) cc_final: 0.6783 (t-100)
REVERT: A  475 LYS cc_start: 0.8400 (tmtt) cc_final: 0.8088 (tptp)
REVERT: A  480 MET cc_start: 0.8615 (mmm) cc_final: 0.8192 (mmm)
REVERT: A  484 ILE cc_start: 0.8632 (mt) cc_final: 0.8327 (mt)
REVERT: A  518 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7497 (tmm-80)
REVERT: A  534 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8406 (mmmm)
REVERT: A  557 MET cc_start: 0.7788 (tmm) cc_final: 0.7474 (tmm)
REVERT: A  559 ARG cc_start: 0.8221 (ptt180) cc_final: 0.7935 (ptm160)
REVERT: A  574 VAL cc_start: 0.9050 (m) cc_final: 0.8768 (p)
REVERT: A  582 ARG cc_start: 0.7466 (tpp80) cc_final: 0.7073 (tpp80)
REVERT: A  598 GLN cc_start: 0.8410 (tt0) cc_final: 0.8117 (tm-30)
REVERT: A  603 PHE cc_start: 0.7223 (t80) cc_final: 0.6873 (t80)
  outliers start: 26
  outliers final: 17
  residues processed: 224
  average time/residue: 0.0997
  time to fit residues: 27.7721
Evaluate side-chains
  241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 219
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  472 ILE
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  608 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 70 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 474 GLN
A  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.107782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.092392 restraints weight = 12278.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.095999 restraints weight = 5716.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.098334 restraints weight = 3246.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.099875 restraints weight = 2107.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100907 restraints weight = 1518.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.5210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6618  Z= 0.229
  Angle     :  0.751   8.658   9000  Z= 0.375
  Chirality :  0.049   0.147    939
  Planarity :  0.004   0.042   1166
  Dihedral  :  5.138  48.532    861
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 28.02 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.30), residues: 787
  helix: -0.73 (0.27), residues: 370
  sheet: -1.89 (0.62), residues: 51
  loop : -0.39 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.021   0.002   TYR E 501 
 PHE   0.026   0.002   PHE A 315 
 TRP   0.017   0.002   TRP E 436 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 6611)
  covalent geometry    : angle       0.74629 ( 8986)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       2.32894 (   14)
  hydrogen bonds       : bond        0.04341 (  200)
  hydrogen bonds       : angle       4.69326 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 218
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7982 (ttp80)
REVERT: E  422 ASN cc_start: 0.8288 (m110) cc_final: 0.7943 (m-40)
REVERT: E  442 ASP cc_start: 0.8677 (t70) cc_final: 0.8121 (t0)
REVERT: E  494 SER cc_start: 0.8834 (m) cc_final: 0.8309 (p)
REVERT: E  505 HIS cc_start: 0.8315 (m170) cc_final: 0.7925 (m170)
REVERT: A   23 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7421 (mt-10)
REVERT: A   26 LYS cc_start: 0.8312 (mttt) cc_final: 0.7970 (mmtt)
REVERT: A   31 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7159 (tttp)
REVERT: A   40 PHE cc_start: 0.8631 (t80) cc_final: 0.8373 (t80)
REVERT: A   47 SER cc_start: 0.8777 (t) cc_final: 0.8401 (p)
REVERT: A   55 THR cc_start: 0.7980 (m) cc_final: 0.7440 (p)
REVERT: A   62 MET cc_start: 0.8297 (tmm) cc_final: 0.7419 (tmm)
REVERT: A   63 ASN cc_start: 0.8739 (m-40) cc_final: 0.8505 (m-40)
REVERT: A  102 GLN cc_start: 0.8584 (pp30) cc_final: 0.8366 (pp30)
REVERT: A  121 ASN cc_start: 0.8928 (m-40) cc_final: 0.8634 (m110)
REVERT: A  163 TRP cc_start: 0.7705 (t60) cc_final: 0.7425 (t60)
REVERT: A  186 LEU cc_start: 0.8489 (tp) cc_final: 0.8184 (tp)
REVERT: A  189 GLU cc_start: 0.7687 (tp30) cc_final: 0.7411 (tp30)
REVERT: A  204 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7854 (mtm-85)
REVERT: A  227 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7639 (tp30)
REVERT: A  249 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7286 (tmm)
REVERT: A  271 TRP cc_start: 0.4964 (t60) cc_final: 0.3767 (t60)
REVERT: A  273 ARG cc_start: 0.8522 (ttt90) cc_final: 0.8224 (ttt90)
REVERT: A  299 ASP cc_start: 0.8313 (t0) cc_final: 0.8068 (t0)
REVERT: A  307 ILE cc_start: 0.8484 (tp) cc_final: 0.8235 (tt)
REVERT: A  310 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7257 (mm-30)
REVERT: A  312 GLU cc_start: 0.7389 (tp30) cc_final: 0.7032 (tp30)
REVERT: A  315 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6916 (t80)
REVERT: A  353 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7989 (mtpt)
REVERT: A  441 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (mmmt)
REVERT: A  446 ILE cc_start: 0.8732 (mm) cc_final: 0.8462 (mt)
REVERT: A  465 LYS cc_start: 0.8799 (mttt) cc_final: 0.8305 (ttmt)
REVERT: A  473 TRP cc_start: 0.7513 (t-100) cc_final: 0.6662 (t-100)
REVERT: A  480 MET cc_start: 0.8710 (mmm) cc_final: 0.8427 (mmm)
REVERT: A  484 ILE cc_start: 0.8727 (mt) cc_final: 0.8334 (mm)
REVERT: A  493 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7296 (m170)
REVERT: A  504 PHE cc_start: 0.8094 (t80) cc_final: 0.7728 (t80)
REVERT: A  518 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7582 (tmm-80)
REVERT: A  534 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8409 (mmmm)
REVERT: A  559 ARG cc_start: 0.8246 (ptt180) cc_final: 0.7962 (ptm160)
REVERT: A  564 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7915 (tt0)
REVERT: A  574 VAL cc_start: 0.9026 (m) cc_final: 0.8790 (p)
REVERT: A  582 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7119 (tpp80)
REVERT: A  603 PHE cc_start: 0.7258 (t80) cc_final: 0.6907 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 230
  average time/residue: 0.0921
  time to fit residues: 26.6920
Evaluate side-chains
  238 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  428 ASP
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  493 HIS
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  608 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0870
   chunk 55 optimal weight:    0.0870
   chunk 45 optimal weight:    0.0070
   chunk 50 optimal weight:    0.0030
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.0764

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 474 GLN
A  33 ASN
A 380 GLN
A 505 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.114478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098726 restraints weight = 12056.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.102471 restraints weight = 5647.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.104861 restraints weight = 3213.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106419 restraints weight = 2086.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107495 restraints weight = 1507.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6618  Z= 0.129
  Angle     :  0.730   9.450   9000  Z= 0.360
  Chirality :  0.044   0.144    939
  Planarity :  0.004   0.046   1166
  Dihedral  :  4.862  46.601    861
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.29 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 29.89 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.30), residues: 787
  helix: -0.56 (0.27), residues: 370
  sheet: -1.31 (0.70), residues: 39
  loop : -0.39 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.022   0.001   TYR E 501 
 PHE   0.017   0.001   PHE A 315 
 TRP   0.013   0.001   TRP A 478 
 HIS   0.004   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6611)
  covalent geometry    : angle       0.72742 ( 8986)
  SS BOND              : bond        0.00319 (    7)
  SS BOND              : angle       1.81259 (   14)
  hydrogen bonds       : bond        0.03692 (  200)
  hydrogen bonds       : angle       4.48782 (  555)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 218
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7854 (ttp80)
REVERT: E  422 ASN cc_start: 0.8213 (m110) cc_final: 0.7925 (m-40)
REVERT: E  442 ASP cc_start: 0.8657 (t70) cc_final: 0.8192 (t0)
REVERT: E  494 SER cc_start: 0.8716 (m) cc_final: 0.8289 (p)
REVERT: E  505 HIS cc_start: 0.8074 (m170) cc_final: 0.7693 (m170)
REVERT: A   26 LYS cc_start: 0.8237 (mttt) cc_final: 0.7874 (mmmm)
REVERT: A   31 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7202 (tttp)
REVERT: A   40 PHE cc_start: 0.8574 (t80) cc_final: 0.8259 (t80)
REVERT: A   42 GLN cc_start: 0.8412 (tt0) cc_final: 0.8143 (tt0)
REVERT: A   47 SER cc_start: 0.8760 (t) cc_final: 0.8394 (p)
REVERT: A   55 THR cc_start: 0.7872 (m) cc_final: 0.7349 (p)
REVERT: A   62 MET cc_start: 0.8294 (tmm) cc_final: 0.7422 (tmm)
REVERT: A   81 GLN cc_start: 0.8208 (tp40) cc_final: 0.7996 (tp40)
REVERT: A   82 MET cc_start: 0.7654 (tpp) cc_final: 0.7408 (tpt)
REVERT: A  102 GLN cc_start: 0.8552 (pp30) cc_final: 0.8347 (pp30)
REVERT: A  179 LEU cc_start: 0.9035 (tp) cc_final: 0.8813 (tt)
REVERT: A  186 LEU cc_start: 0.8240 (tp) cc_final: 0.8030 (tp)
REVERT: A  189 GLU cc_start: 0.7667 (tp30) cc_final: 0.7418 (tp30)
REVERT: A  204 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7801 (mtm-85)
REVERT: A  227 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7554 (tp30)
REVERT: A  271 TRP cc_start: 0.4988 (t60) cc_final: 0.4002 (t60)
REVERT: A  273 ARG cc_start: 0.8404 (ttt90) cc_final: 0.8143 (ttt90)
REVERT: A  299 ASP cc_start: 0.8268 (t0) cc_final: 0.7955 (t0)
REVERT: A  307 ILE cc_start: 0.8309 (tp) cc_final: 0.8067 (tt)
REVERT: A  310 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7222 (mm-30)
REVERT: A  312 GLU cc_start: 0.7350 (tp30) cc_final: 0.7064 (tp30)
REVERT: A  315 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7051 (t80)
REVERT: A  332 MET cc_start: 0.7951 (tmm) cc_final: 0.7744 (ppp)
REVERT: A  353 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7867 (mtpt)
REVERT: A  380 GLN cc_start: 0.7698 (mt0) cc_final: 0.7430 (mt0)
REVERT: A  465 LYS cc_start: 0.8614 (mttt) cc_final: 0.8140 (tppp)
REVERT: A  473 TRP cc_start: 0.7399 (t-100) cc_final: 0.7176 (t-100)
REVERT: A  480 MET cc_start: 0.8572 (mmm) cc_final: 0.8169 (mmm)
REVERT: A  484 ILE cc_start: 0.8660 (mt) cc_final: 0.8384 (mt)
REVERT: A  504 PHE cc_start: 0.7977 (t80) cc_final: 0.7728 (t80)
REVERT: A  534 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8418 (mmmm)
REVERT: A  559 ARG cc_start: 0.8119 (ptt180) cc_final: 0.7798 (ptm160)
REVERT: A  564 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7739 (tt0)
REVERT: A  574 VAL cc_start: 0.9010 (m) cc_final: 0.8766 (p)
REVERT: A  582 ARG cc_start: 0.7423 (tpp80) cc_final: 0.7060 (tpp80)
REVERT: A  603 PHE cc_start: 0.7164 (t80) cc_final: 0.6835 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 227
  average time/residue: 0.0877
  time to fit residues: 25.3455
Evaluate side-chains
  221 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 206
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  608 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5036 > 50:
  distance: 102 - 103:  10.424
  distance: 103 - 104:   6.094
  distance: 103 - 106:   3.306
  distance: 104 - 105:  19.299
  distance: 104 - 109:  15.667
  distance: 106 - 107:  15.033
  distance: 106 - 108:  33.049
  distance: 110 - 111:  12.201
  distance: 110 - 113:  19.843
  distance: 111 - 112:  11.286
  distance: 111 - 118:  10.865
  distance: 113 - 114:   7.046
  distance: 114 - 115:  15.071
  distance: 115 - 116:  20.829
  distance: 115 - 117:  30.977
  distance: 118 - 119:  12.759
  distance: 118 - 124:  14.595
  distance: 119 - 120:  18.791
  distance: 119 - 122:  15.169
  distance: 120 - 121:  14.308
  distance: 120 - 125:  20.256
  distance: 122 - 123:   7.285
  distance: 123 - 124:  18.956
  distance: 125 - 126:  11.462
  distance: 126 - 127:  16.043
  distance: 126 - 129:  20.976
  distance: 127 - 128:   8.169
  distance: 127 - 132:   5.168
  distance: 129 - 130:  15.766
  distance: 129 - 131:  44.863
  distance: 132 - 133:   5.656
  distance: 132 - 138:  14.727
  distance: 133 - 134:  15.477
  distance: 133 - 136:  16.177
  distance: 134 - 139:  12.895
  distance: 136 - 137:  10.195
  distance: 137 - 138:   8.811
  distance: 139 - 140:  11.869
  distance: 140 - 141:  12.032
  distance: 140 - 143:   9.458
  distance: 141 - 142:  11.889
  distance: 141 - 149:  13.933
  distance: 143 - 144:   7.407
  distance: 144 - 145:   6.241
  distance: 144 - 146:   3.741
  distance: 145 - 147:   5.811
  distance: 146 - 148:   5.796
  distance: 147 - 148:   4.359
  distance: 149 - 150:   6.394
  distance: 150 - 151:  14.848
  distance: 150 - 153:  20.246
  distance: 151 - 152:  11.474
  distance: 151 - 157:  15.197
  distance: 153 - 154:  18.165
  distance: 154 - 155:  22.024
  distance: 154 - 156:  10.114
  distance: 157 - 158:   4.178
  distance: 158 - 159:   9.742
  distance: 158 - 161:  14.782
  distance: 159 - 160:   7.805
  distance: 159 - 166:   6.296
  distance: 162 - 163:  18.370
  distance: 163 - 164:  13.084
  distance: 163 - 165:  32.224
  distance: 166 - 167:   3.364
  distance: 167 - 168:   8.405
  distance: 167 - 170:  16.601
  distance: 168 - 169:   6.105
  distance: 168 - 173:   9.291
  distance: 170 - 171:  10.054
  distance: 170 - 172:  18.963
  distance: 174 - 177:   4.161
  distance: 175 - 176:   5.743
  distance: 175 - 185:   5.865
  distance: 177 - 178:   9.642
  distance: 178 - 179:   4.611
  distance: 178 - 180:   7.387
  distance: 179 - 181:   8.816
  distance: 180 - 182:   6.225
  distance: 181 - 183:   4.321
  distance: 182 - 183:   9.979
  distance: 183 - 184:   6.509