Starting phenix.real_space_refine
on Thu Jun  5 15:59:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wk6_32560/06_2025/7wk6_32560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wk6_32560/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wk6_32560/06_2025/7wk6_32560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wk6_32560/06_2025/7wk6_32560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wk6_32560/06_2025/7wk6_32560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wk6_32560/06_2025/7wk6_32560.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.11, per 1000 atoms: 0.95
  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: 1.54
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.65
  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: 2.34

  Time building geometry restraints manager: 1.88 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:             21.150
  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:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.410
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.430
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.022   0.002   TRP A 478 
 HIS   0.018   0.002   HIS A  34 
 PHE   0.020   0.002   PHE A  32 
 TYR   0.016   0.002   TYR A 183 
 ARG   0.006   0.001   ARG A 482 

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

*********************** 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  : 0.792 
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: 0.7906 (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: 0.8194 (mp)
REVERT: E  467 ASP cc_start: 0.7953 (p0) cc_final: 0.7526 (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: 0.7783 (tp30)
REVERT: E  474 GLN cc_start: 0.7884 (tt0) cc_final: 0.7632 (tt0)
REVERT: E  492 LEU cc_start: 0.8677 (mt) cc_final: 0.8358 (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: 0.7256 (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: 0.8503 (t0)
REVERT: A  101 GLN cc_start: 0.8013 (tt0) cc_final: 0.7701 (mt0)
REVERT: A  144 LEU cc_start: 0.7666 (tp) cc_final: 0.7360 (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: 0.7753 (t-100)
REVERT: A  181 GLU cc_start: 0.7868 (tp30) cc_final: 0.7609 (tp30)
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: 0.7521 (mm-30)
REVERT: A  265 HIS cc_start: 0.8826 (p-80) cc_final: 0.7984 (p-80)
REVERT: A  271 TRP cc_start: 0.4633 (t60) cc_final: 0.4293 (t60)
REVERT: A  277 ASN cc_start: 0.8575 (m-40) cc_final: 0.8284 (m-40)
REVERT: A  302 TRP cc_start: 0.8349 (m-10) cc_final: 0.7970 (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: 0.7329 (tmm)
REVERT: A  341 LYS cc_start: 0.7902 (tptt) cc_final: 0.7603 (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: 0.7489 (mmp)
REVERT: A  419 LYS cc_start: 0.8243 (tptp) cc_final: 0.8021 (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: 0.7194 (m-40)
REVERT: A  459 TRP cc_start: 0.8262 (t60) cc_final: 0.7979 (t60)
REVERT: A  462 MET cc_start: 0.7529 (mtm) cc_final: 0.7267 (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: 0.6665 (t-100)
REVERT: A  475 LYS cc_start: 0.8865 (tppt) cc_final: 0.8636 (tptp)
REVERT: A  499 ASP cc_start: 0.7772 (m-30) cc_final: 0.6844 (t0)
REVERT: A  500 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.7806 (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: 0.8391 (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: 0.6647 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 252
  average time/residue: 0.2904
  time to fit residues: 91.8299
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  : 0.798 
-------------------------------------------------------------------------------
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 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0000
   chunk 32 optimal weight:    0.0670
   chunk 20 optimal weight:    0.2980
   chunk 39 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 61 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.2722

-------------------------------------------------------------------------------
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 121 ASN
A 330 ASN
A 373 HIS
A 417 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.099218 restraints weight = 11781.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.102723 restraints weight = 5449.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.105006 restraints weight = 3097.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6618  Z= 0.141
  Angle     :  0.624   8.893   9000  Z= 0.325
  Chirality :  0.044   0.124    939
  Planarity :  0.005   0.036   1166
  Dihedral  :  5.368  65.531    864
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.67 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.26), residues: 787
  helix: -3.20 (0.20), residues: 353
  sheet: -1.43 (0.93), residues: 33
  loop : -1.60 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 478 
 HIS   0.003   0.001   HIS E 505 
 PHE   0.011   0.001   PHE E 490 
 TYR   0.016   0.001   TYR A 158 
 ARG   0.004   0.000   ARG E 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05041 (  200)
  hydrogen bonds       : angle       5.51275 (  555)
  SS BOND              : bond        0.00378 (    7)
  SS BOND              : angle       1.46315 (   14)
  covalent geometry    : bond        0.00312 ( 6611)
  covalent geometry    : angle       0.62183 ( 8986)

*********************** 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
  241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 224
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  422 ASN cc_start: 0.8090 (m110) cc_final: 0.7722 (m-40)
REVERT: E  442 ASP cc_start: 0.8756 (t70) cc_final: 0.8285 (t0)
REVERT: E  465 GLU cc_start: 0.7858 (tt0) cc_final: 0.7627 (tt0)
REVERT: E  467 ASP cc_start: 0.7762 (p0) cc_final: 0.7421 (p0)
REVERT: E  489 TYR cc_start: 0.7029 (m-80) cc_final: 0.6827 (m-80)
REVERT: E  494 SER cc_start: 0.8821 (m) cc_final: 0.8378 (p)
REVERT: A   23 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7260 (mp0)
REVERT: A   26 LYS cc_start: 0.8126 (mttt) cc_final: 0.7817 (mmmm)
REVERT: A   40 PHE cc_start: 0.8621 (t80) cc_final: 0.8259 (t80)
REVERT: A   42 GLN cc_start: 0.8277 (tt0) cc_final: 0.8039 (tt0)
REVERT: A   47 SER cc_start: 0.8689 (t) cc_final: 0.8390 (t)
REVERT: A   55 THR cc_start: 0.7790 (m) cc_final: 0.7100 (p)
REVERT: A   62 MET cc_start: 0.7956 (tmm) cc_final: 0.7158 (tmm)
REVERT: A  101 GLN cc_start: 0.7903 (tt0) cc_final: 0.7686 (mt0)
REVERT: A  102 GLN cc_start: 0.7982 (pp30) cc_final: 0.7731 (pp30)
REVERT: A  126 ILE cc_start: 0.8942 (tp) cc_final: 0.8631 (tt)
REVERT: A  144 LEU cc_start: 0.8348 (tp) cc_final: 0.7834 (tp)
REVERT: A  157 ASP cc_start: 0.7924 (m-30) cc_final: 0.7658 (t70)
REVERT: A  158 TYR cc_start: 0.7388 (t80) cc_final: 0.6903 (t80)
REVERT: A  168 TRP cc_start: 0.8266 (t-100) cc_final: 0.7853 (t-100)
REVERT: A  182 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6754 (tm-30)
REVERT: A  186 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8028 (mp)
REVERT: A  209 VAL cc_start: 0.8633 (t) cc_final: 0.8403 (m)
REVERT: A  219 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7822 (mtm-85)
REVERT: A  227 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7728 (tp30)
REVERT: A  267 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8358 (mm)
REVERT: A  271 TRP cc_start: 0.5008 (t60) cc_final: 0.4451 (t60)
REVERT: A  299 ASP cc_start: 0.7959 (t0) cc_final: 0.7733 (t0)
REVERT: A  313 LYS cc_start: 0.8190 (mttt) cc_final: 0.7705 (mtpt)
REVERT: A  325 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7298 (tp-100)
REVERT: A  332 MET cc_start: 0.7986 (ttp) cc_final: 0.7575 (tmm)
REVERT: A  353 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8148 (mmmt)
REVERT: A  368 ASP cc_start: 0.8112 (t0) cc_final: 0.7258 (t0)
REVERT: A  429 GLN cc_start: 0.7373 (tp40) cc_final: 0.7066 (tp40)
REVERT: A  465 LYS cc_start: 0.8661 (mttt) cc_final: 0.8336 (ttmt)
REVERT: A  472 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7541 (mm-40)
REVERT: A  475 LYS cc_start: 0.8327 (tppt) cc_final: 0.8088 (tmtt)
REVERT: A  499 ASP cc_start: 0.8240 (m-30) cc_final: 0.7381 (t0)
REVERT: A  500 PRO cc_start: 0.8815 (Cg_endo) cc_final: 0.8551 (Cg_exo)
REVERT: A  504 PHE cc_start: 0.7949 (t80) cc_final: 0.7700 (t80)
REVERT: A  574 VAL cc_start: 0.8977 (m) cc_final: 0.8721 (p)
REVERT: A  582 ARG cc_start: 0.7448 (tpp80) cc_final: 0.6964 (mpp80)
REVERT: A  603 PHE cc_start: 0.6920 (t80) cc_final: 0.6576 (t80)
  outliers start: 17
  outliers final: 5
  residues processed: 235
  average time/residue: 0.3232
  time to fit residues: 98.7565
Evaluate side-chains
  222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 215
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0020
   chunk 54 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.4188

-------------------------------------------------------------------------------
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 401 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.112148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.096825 restraints weight = 12018.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.100370 restraints weight = 5540.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.102622 restraints weight = 3127.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6618  Z= 0.171
  Angle     :  0.642   9.494   9000  Z= 0.326
  Chirality :  0.045   0.122    939
  Planarity :  0.004   0.046   1166
  Dihedral  :  4.988  58.208    861
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.12 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.28), residues: 787
  helix: -2.44 (0.23), residues: 362
  sheet: -1.41 (0.87), residues: 34
  loop : -1.16 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 436 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.028   0.002   PHE A 428 
 TYR   0.016   0.001   TYR A 215 
 ARG   0.006   0.000   ARG E 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04613 (  200)
  hydrogen bonds       : angle       4.82848 (  555)
  SS BOND              : bond        0.00573 (    7)
  SS BOND              : angle       1.68770 (   14)
  covalent geometry    : bond        0.00381 ( 6611)
  covalent geometry    : angle       0.63940 ( 8986)

*********************** 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
  240 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 220
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  335 LEU cc_start: 0.8469 (tp) cc_final: 0.8248 (tp)
REVERT: E  442 ASP cc_start: 0.8719 (t70) cc_final: 0.8234 (t0)
REVERT: E  467 ASP cc_start: 0.7801 (p0) cc_final: 0.7491 (p0)
REVERT: E  473 TYR cc_start: 0.7685 (t80) cc_final: 0.7370 (t80)
REVERT: E  489 TYR cc_start: 0.7334 (m-80) cc_final: 0.7080 (m-80)
REVERT: E  494 SER cc_start: 0.8822 (m) cc_final: 0.8318 (p)
REVERT: A   23 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7346 (mp0)
REVERT: A   26 LYS cc_start: 0.8195 (mttt) cc_final: 0.7925 (mmtt)
REVERT: A   40 PHE cc_start: 0.8711 (t80) cc_final: 0.8358 (t80)
REVERT: A   47 SER cc_start: 0.8780 (t) cc_final: 0.8485 (t)
REVERT: A   55 THR cc_start: 0.7781 (m) cc_final: 0.7120 (p)
REVERT: A   62 MET cc_start: 0.7995 (tmm) cc_final: 0.7193 (tmm)
REVERT: A  101 GLN cc_start: 0.7869 (tt0) cc_final: 0.7652 (tt0)
REVERT: A  102 GLN cc_start: 0.8190 (pp30) cc_final: 0.7926 (pp30)
REVERT: A  105 SER cc_start: 0.8395 (p) cc_final: 0.8035 (t)
REVERT: A  126 ILE cc_start: 0.8946 (tp) cc_final: 0.8624 (tt)
REVERT: A  144 LEU cc_start: 0.8371 (tp) cc_final: 0.7833 (tp)
REVERT: A  157 ASP cc_start: 0.7939 (m-30) cc_final: 0.7682 (t0)
REVERT: A  158 TYR cc_start: 0.7583 (t80) cc_final: 0.6976 (t80)
REVERT: A  166 GLU cc_start: 0.7484 (tp30) cc_final: 0.7251 (tp30)
REVERT: A  168 TRP cc_start: 0.8340 (t-100) cc_final: 0.7865 (t-100)
REVERT: A  182 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7099 (tm-30)
REVERT: A  204 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8233 (mtm180)
REVERT: A  224 GLU cc_start: 0.7818 (tp30) cc_final: 0.7601 (tp30)
REVERT: A  227 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7643 (tp30)
REVERT: A  245 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8206 (mtp-110)
REVERT: A  267 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8289 (mt)
REVERT: A  271 TRP cc_start: 0.4941 (t60) cc_final: 0.4296 (t60)
REVERT: A  299 ASP cc_start: 0.8012 (t0) cc_final: 0.7718 (t0)
REVERT: A  313 LYS cc_start: 0.8160 (mttt) cc_final: 0.7865 (mtpt)
REVERT: A  320 LEU cc_start: 0.8919 (mm) cc_final: 0.8490 (mt)
REVERT: A  323 MET cc_start: 0.8326 (mmt) cc_final: 0.8039 (mmt)
REVERT: A  353 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8070 (mmmt)
REVERT: A  363 LYS cc_start: 0.8794 (mppt) cc_final: 0.8425 (mppt)
REVERT: A  368 ASP cc_start: 0.8008 (t0) cc_final: 0.7805 (t0)
REVERT: A  380 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8241 (mt0)
REVERT: A  406 GLU cc_start: 0.7851 (tp30) cc_final: 0.7530 (tp30)
REVERT: A  429 GLN cc_start: 0.7425 (tp40) cc_final: 0.7134 (tp40)
REVERT: A  465 LYS cc_start: 0.8825 (mttt) cc_final: 0.8440 (ttmt)
REVERT: A  472 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7511 (mm-40)
REVERT: A  475 LYS cc_start: 0.8449 (tppt) cc_final: 0.8192 (tmtt)
REVERT: A  504 PHE cc_start: 0.8086 (t80) cc_final: 0.7778 (t80)
REVERT: A  514 ARG cc_start: 0.8123 (mtm180) cc_final: 0.7895 (mtm110)
REVERT: A  559 ARG cc_start: 0.8152 (ptt180) cc_final: 0.7893 (ptm160)
REVERT: A  574 VAL cc_start: 0.8995 (m) cc_final: 0.8779 (p)
REVERT: A  603 PHE cc_start: 0.7058 (t80) cc_final: 0.6673 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 228
  average time/residue: 0.2303
  time to fit residues: 65.3281
Evaluate side-chains
  218 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 207
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  415 THR
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  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
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 14 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   chunk 7 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.110001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.094771 restraints weight = 12370.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.098345 restraints weight = 5702.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.100591 restraints weight = 3210.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3901

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= 0.180
  Angle     :  0.668  10.132   9000  Z= 0.336
  Chirality :  0.045   0.141    939
  Planarity :  0.004   0.046   1166
  Dihedral  :  4.940  54.809    861
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.84 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.28), residues: 787
  helix: -2.06 (0.24), residues: 366
  sheet: -1.33 (0.86), residues: 36
  loop : -0.93 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.018   0.002   PHE A 400 
 TYR   0.026   0.002   TYR A 158 
 ARG   0.007   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04329 (  200)
  hydrogen bonds       : angle       4.67681 (  555)
  SS BOND              : bond        0.00333 (    7)
  SS BOND              : angle       2.11351 (   14)
  covalent geometry    : bond        0.00405 ( 6611)
  covalent geometry    : angle       0.66343 ( 8986)

*********************** 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
  232 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 211
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.8846 (m-10) cc_final: 0.8482 (m-80)
REVERT: E  357 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7735 (mtp85)
REVERT: E  403 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7458 (ptm-80)
REVERT: E  422 ASN cc_start: 0.8191 (m110) cc_final: 0.7865 (m-40)
REVERT: E  442 ASP cc_start: 0.8706 (t70) cc_final: 0.8255 (t0)
REVERT: E  494 SER cc_start: 0.8836 (m) cc_final: 0.8336 (p)
REVERT: E  505 HIS cc_start: 0.8361 (m170) cc_final: 0.8029 (m170)
REVERT: E  517 LEU cc_start: 0.8681 (mm) cc_final: 0.8253 (mp)
REVERT: A   23 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7322 (mp0)
REVERT: A   26 LYS cc_start: 0.8254 (mttt) cc_final: 0.7938 (mmtt)
REVERT: A   40 PHE cc_start: 0.8681 (t80) cc_final: 0.8356 (t80)
REVERT: A   47 SER cc_start: 0.8776 (t) cc_final: 0.8378 (p)
REVERT: A   55 THR cc_start: 0.7822 (m) cc_final: 0.7179 (p)
REVERT: A   62 MET cc_start: 0.8104 (tmm) cc_final: 0.7263 (tmm)
REVERT: A  101 GLN cc_start: 0.7913 (tt0) cc_final: 0.7431 (tp40)
REVERT: A  102 GLN cc_start: 0.8392 (pp30) cc_final: 0.8047 (pp30)
REVERT: A  110 GLU cc_start: 0.7248 (tp30) cc_final: 0.6958 (tp30)
REVERT: A  121 ASN cc_start: 0.8539 (m-40) cc_final: 0.8306 (m-40)
REVERT: A  123 MET cc_start: 0.8205 (ttt) cc_final: 0.7724 (ttp)
REVERT: A  126 ILE cc_start: 0.8845 (tp) cc_final: 0.8603 (tt)
REVERT: A  144 LEU cc_start: 0.8349 (tp) cc_final: 0.7750 (tp)
REVERT: A  157 ASP cc_start: 0.7883 (m-30) cc_final: 0.7638 (t0)
REVERT: A  168 TRP cc_start: 0.8372 (t-100) cc_final: 0.7807 (t-100)
REVERT: A  182 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6938 (tm-30)
REVERT: A  204 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8272 (mtm180)
REVERT: A  224 GLU cc_start: 0.7894 (tp30) cc_final: 0.7617 (tp30)
REVERT: A  227 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7683 (tp30)
REVERT: A  267 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8277 (mt)
REVERT: A  271 TRP cc_start: 0.5051 (t60) cc_final: 0.4204 (t60)
REVERT: A  299 ASP cc_start: 0.8162 (t0) cc_final: 0.7848 (t0)
REVERT: A  313 LYS cc_start: 0.8050 (mttt) cc_final: 0.7827 (mtpt)
REVERT: A  323 MET cc_start: 0.8374 (mmt) cc_final: 0.8152 (mmt)
REVERT: A  332 MET cc_start: 0.7801 (tmm) cc_final: 0.7470 (tmm)
REVERT: A  353 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8068 (mtpt)
REVERT: A  363 LYS cc_start: 0.8785 (mppt) cc_final: 0.8394 (mppt)
REVERT: A  375 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7587 (mm-30)
REVERT: A  406 GLU cc_start: 0.7903 (tp30) cc_final: 0.7632 (tp30)
REVERT: A  429 GLN cc_start: 0.7445 (tp40) cc_final: 0.7090 (tp40)
REVERT: A  465 LYS cc_start: 0.8826 (mttt) cc_final: 0.8409 (ttmt)
REVERT: A  472 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7575 (mm-40)
REVERT: A  473 TRP cc_start: 0.7540 (t-100) cc_final: 0.6588 (t-100)
REVERT: A  475 LYS cc_start: 0.8324 (tppt) cc_final: 0.8096 (tmtt)
REVERT: A  483 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6922 (tm-30)
REVERT: A  484 ILE cc_start: 0.8727 (mt) cc_final: 0.8281 (mm)
REVERT: A  495 GLU cc_start: 0.6710 (tm-30) cc_final: 0.6475 (tp30)
REVERT: A  504 PHE cc_start: 0.8108 (t80) cc_final: 0.7729 (t80)
REVERT: A  557 MET cc_start: 0.7948 (tmm) cc_final: 0.7692 (tmm)
REVERT: A  559 ARG cc_start: 0.8179 (ptt180) cc_final: 0.7851 (ptm160)
REVERT: A  574 VAL cc_start: 0.9018 (m) cc_final: 0.8788 (p)
REVERT: A  577 LYS cc_start: 0.8926 (ptpp) cc_final: 0.8608 (ptpp)
REVERT: A  582 ARG cc_start: 0.7533 (tpp80) cc_final: 0.7089 (tpp80)
REVERT: A  603 PHE cc_start: 0.7165 (t80) cc_final: 0.6775 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 220
  average time/residue: 0.2306
  time to fit residues: 63.1764
Evaluate side-chains
  224 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 209
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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  180 TYR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  203 TRP
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  401 HIS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.107732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.092701 restraints weight = 12138.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.096154 restraints weight = 5613.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.098370 restraints weight = 3177.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6618  Z= 0.256
  Angle     :  0.715   9.666   9000  Z= 0.360
  Chirality :  0.048   0.145    939
  Planarity :  0.004   0.043   1166
  Dihedral  :  5.184  53.710    861
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.67 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.00 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.29), residues: 787
  helix: -1.81 (0.24), residues: 362
  sheet: -1.41 (0.84), residues: 36
  loop : -0.81 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 436 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.019   0.002   PHE A 400 
 TYR   0.028   0.002   TYR A 158 
 ARG   0.005   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  200)
  hydrogen bonds       : angle       4.90182 (  555)
  SS BOND              : bond        0.00352 (    7)
  SS BOND              : angle       2.78391 (   14)
  covalent geometry    : bond        0.00568 ( 6611)
  covalent geometry    : angle       0.70740 ( 8986)

*********************** 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
  242 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7765 (ttp80)
REVERT: E  380 TYR cc_start: 0.8976 (m-80) cc_final: 0.8708 (m-80)
REVERT: E  403 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7638 (ptm-80)
REVERT: E  422 ASN cc_start: 0.8143 (m110) cc_final: 0.7650 (m-40)
REVERT: E  442 ASP cc_start: 0.8663 (t70) cc_final: 0.8143 (t0)
REVERT: E  494 SER cc_start: 0.8917 (m) cc_final: 0.8426 (p)
REVERT: E  495 TYR cc_start: 0.8571 (m-10) cc_final: 0.8345 (m-80)
REVERT: E  505 HIS cc_start: 0.8458 (m170) cc_final: 0.8211 (m170)
REVERT: E  517 LEU cc_start: 0.8719 (mm) cc_final: 0.8400 (mt)
REVERT: A   23 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7229 (mp0)
REVERT: A   26 LYS cc_start: 0.8235 (mttt) cc_final: 0.7906 (mmtt)
REVERT: A   47 SER cc_start: 0.8797 (t) cc_final: 0.8432 (p)
REVERT: A   55 THR cc_start: 0.7955 (m) cc_final: 0.7368 (p)
REVERT: A   62 MET cc_start: 0.8176 (tmm) cc_final: 0.7299 (tmm)
REVERT: A  101 GLN cc_start: 0.7929 (tt0) cc_final: 0.7655 (tt0)
REVERT: A  102 GLN cc_start: 0.8543 (pp30) cc_final: 0.8228 (pp30)
REVERT: A  110 GLU cc_start: 0.7149 (tp30) cc_final: 0.6738 (tp30)
REVERT: A  121 ASN cc_start: 0.8727 (m-40) cc_final: 0.8429 (m110)
REVERT: A  123 MET cc_start: 0.8374 (ttt) cc_final: 0.8025 (ttp)
REVERT: A  126 ILE cc_start: 0.8929 (tp) cc_final: 0.8675 (tt)
REVERT: A  144 LEU cc_start: 0.8360 (tp) cc_final: 0.7753 (tp)
REVERT: A  160 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6931 (tm-30)
REVERT: A  163 TRP cc_start: 0.7562 (t60) cc_final: 0.7321 (t60)
REVERT: A  166 GLU cc_start: 0.7236 (tp30) cc_final: 0.6986 (tp30)
REVERT: A  168 TRP cc_start: 0.8428 (t-100) cc_final: 0.7922 (t-100)
REVERT: A  182 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: A  186 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8271 (mp)
REVERT: A  204 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8152 (mtm180)
REVERT: A  227 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7693 (tp30)
REVERT: A  249 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7163 (tmm)
REVERT: A  267 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8374 (mt)
REVERT: A  271 TRP cc_start: 0.5103 (t60) cc_final: 0.4161 (t60)
REVERT: A  299 ASP cc_start: 0.8238 (t0) cc_final: 0.7972 (t0)
REVERT: A  313 LYS cc_start: 0.8109 (mttt) cc_final: 0.7868 (ttmm)
REVERT: A  323 MET cc_start: 0.8561 (mmt) cc_final: 0.8202 (mmt)
REVERT: A  332 MET cc_start: 0.7878 (tmm) cc_final: 0.7546 (tmm)
REVERT: A  353 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8103 (mtpt)
REVERT: A  375 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7468 (mm-30)
REVERT: A  406 GLU cc_start: 0.7982 (tp30) cc_final: 0.7745 (tp30)
REVERT: A  429 GLN cc_start: 0.7481 (tp40) cc_final: 0.7125 (tp40)
REVERT: A  465 LYS cc_start: 0.8838 (mttt) cc_final: 0.8295 (ttmt)
REVERT: A  480 MET cc_start: 0.8773 (mmm) cc_final: 0.8422 (mmm)
REVERT: A  518 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7674 (tmm-80)
REVERT: A  557 MET cc_start: 0.7952 (tmm) cc_final: 0.7653 (tmm)
REVERT: A  559 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7962 (ptm160)
REVERT: A  574 VAL cc_start: 0.9038 (m) cc_final: 0.8774 (p)
REVERT: A  577 LYS cc_start: 0.8870 (ptpp) cc_final: 0.8633 (ptpp)
REVERT: A  582 ARG cc_start: 0.7576 (tpp80) cc_final: 0.7161 (tpp80)
REVERT: A  603 PHE cc_start: 0.7240 (t80) cc_final: 0.6873 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 226
  average time/residue: 0.2396
  time to fit residues: 67.4293
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  : 0.793 
-------------------------------------------------------------------------------
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   37 GLU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  186 LEU
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  267 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  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  608 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0370
   chunk 36 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   overall best weight:    0.2056

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

Flipped N/Q/H residues before XYZ refinement:
E 394 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.112396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.097102 restraints weight = 11960.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100658 restraints weight = 5539.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.102899 restraints weight = 3128.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6618  Z= 0.126
  Angle     :  0.661  11.405   9000  Z= 0.327
  Chirality :  0.044   0.138    939
  Planarity :  0.004   0.049   1166
  Dihedral  :  4.857  51.808    861
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.16 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 26.44 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.29), residues: 787
  helix: -1.37 (0.26), residues: 364
  sheet: -1.44 (0.82), residues: 35
  loop : -0.68 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 478 
 HIS   0.002   0.000   HIS A 374 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.019   0.001   TYR A 158 
 ARG   0.004   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  200)
  hydrogen bonds       : angle       4.54071 (  555)
  SS BOND              : bond        0.00169 (    7)
  SS BOND              : angle       2.26096 (   14)
  covalent geometry    : bond        0.00296 ( 6611)
  covalent geometry    : angle       0.65516 ( 8986)

*********************** 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
  233 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.8697 (m-80) cc_final: 0.8490 (m-10)
REVERT: E  403 ARG cc_start: 0.8380 (ttp80) cc_final: 0.7564 (ptm-80)
REVERT: E  422 ASN cc_start: 0.8103 (m110) cc_final: 0.7825 (m110)
REVERT: E  442 ASP cc_start: 0.8656 (t70) cc_final: 0.8152 (t0)
REVERT: E  494 SER cc_start: 0.8803 (m) cc_final: 0.8328 (p)
REVERT: E  505 HIS cc_start: 0.8196 (m170) cc_final: 0.7912 (m170)
REVERT: E  517 LEU cc_start: 0.8626 (mm) cc_final: 0.8412 (mp)
REVERT: A   23 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7168 (mp0)
REVERT: A   29 LEU cc_start: 0.8457 (mt) cc_final: 0.8193 (mt)
REVERT: A   40 PHE cc_start: 0.8618 (t80) cc_final: 0.8323 (t80)
REVERT: A   47 SER cc_start: 0.8778 (t) cc_final: 0.8391 (p)
REVERT: A   55 THR cc_start: 0.7887 (m) cc_final: 0.7292 (p)
REVERT: A   62 MET cc_start: 0.8169 (tmm) cc_final: 0.7291 (tmm)
REVERT: A   81 GLN cc_start: 0.7997 (tp40) cc_final: 0.7795 (tp40)
REVERT: A  101 GLN cc_start: 0.7881 (tt0) cc_final: 0.7534 (tp40)
REVERT: A  102 GLN cc_start: 0.8539 (pp30) cc_final: 0.8282 (pp30)
REVERT: A  121 ASN cc_start: 0.8752 (m-40) cc_final: 0.8429 (m-40)
REVERT: A  123 MET cc_start: 0.8365 (ttt) cc_final: 0.7777 (ttp)
REVERT: A  126 ILE cc_start: 0.8840 (tp) cc_final: 0.8619 (tt)
REVERT: A  163 TRP cc_start: 0.7380 (t60) cc_final: 0.7177 (t60)
REVERT: A  166 GLU cc_start: 0.7046 (tp30) cc_final: 0.6816 (tp30)
REVERT: A  182 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6686 (tm-30)
REVERT: A  186 LEU cc_start: 0.8580 (tp) cc_final: 0.8197 (mp)
REVERT: A  204 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.7934 (mtm180)
REVERT: A  227 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7647 (tp30)
REVERT: A  267 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8275 (mt)
REVERT: A  271 TRP cc_start: 0.4969 (t60) cc_final: 0.4310 (t60)
REVERT: A  299 ASP cc_start: 0.8210 (t0) cc_final: 0.7915 (t0)
REVERT: A  313 LYS cc_start: 0.7937 (mttt) cc_final: 0.7710 (mtpt)
REVERT: A  325 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: A  330 ASN cc_start: 0.8164 (p0) cc_final: 0.7949 (p0)
REVERT: A  332 MET cc_start: 0.7761 (tmm) cc_final: 0.7439 (tmm)
REVERT: A  353 LYS cc_start: 0.8300 (mtpt) cc_final: 0.8098 (mmmt)
REVERT: A  375 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7496 (mm-30)
REVERT: A  406 GLU cc_start: 0.7953 (tp30) cc_final: 0.7723 (tp30)
REVERT: A  465 LYS cc_start: 0.8730 (mttt) cc_final: 0.8278 (ttmt)
REVERT: A  480 MET cc_start: 0.8706 (mmm) cc_final: 0.8352 (mmm)
REVERT: A  483 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6884 (tm-30)
REVERT: A  484 ILE cc_start: 0.8716 (mt) cc_final: 0.8297 (mm)
REVERT: A  499 ASP cc_start: 0.8479 (m-30) cc_final: 0.8156 (t0)
REVERT: A  518 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7479 (tmm-80)
REVERT: A  557 MET cc_start: 0.7825 (tmm) cc_final: 0.7545 (tmm)
REVERT: A  559 ARG cc_start: 0.8270 (ptt180) cc_final: 0.7925 (ptm160)
REVERT: A  574 VAL cc_start: 0.9058 (m) cc_final: 0.8768 (p)
REVERT: A  577 LYS cc_start: 0.8851 (ptpp) cc_final: 0.8589 (ptpp)
REVERT: A  582 ARG cc_start: 0.7460 (tpp80) cc_final: 0.7077 (tpp80)
REVERT: A  603 PHE cc_start: 0.7180 (t80) cc_final: 0.6807 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 219
  average time/residue: 0.2301
  time to fit residues: 62.7028
Evaluate side-chains
  222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  359 SER
Chi-restraints excluded: chain E residue  472 ILE
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  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  267 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  380 GLN
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  468 ILE
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 25 optimal weight:    0.0870
   chunk 74 optimal weight:    0.1980
   chunk 50 optimal weight:    0.0370
   chunk 64 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.110989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.096052 restraints weight = 12020.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.099570 restraints weight = 5579.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.101810 restraints weight = 3152.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6618  Z= 0.156
  Angle     :  0.689   9.924   9000  Z= 0.341
  Chirality :  0.045   0.124    939
  Planarity :  0.004   0.048   1166
  Dihedral  :  4.832  50.102    861
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.54 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 27.30 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.30), residues: 787
  helix: -1.14 (0.26), residues: 367
  sheet: -1.43 (0.79), residues: 35
  loop : -0.53 (0.34), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.015   0.001   PHE A 400 
 TYR   0.014   0.002   TYR A 158 
 ARG   0.007   0.001   ARG E 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  200)
  hydrogen bonds       : angle       4.54608 (  555)
  SS BOND              : bond        0.00264 (    7)
  SS BOND              : angle       2.46379 (   14)
  covalent geometry    : bond        0.00362 ( 6611)
  covalent geometry    : angle       0.68238 ( 8986)

*********************** 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
  232 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 208
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7639 (ptm-80)
REVERT: E  422 ASN cc_start: 0.8168 (m110) cc_final: 0.7861 (m110)
REVERT: E  442 ASP cc_start: 0.8631 (t70) cc_final: 0.8129 (t0)
REVERT: E  494 SER cc_start: 0.8774 (m) cc_final: 0.8298 (p)
REVERT: E  505 HIS cc_start: 0.8240 (m170) cc_final: 0.7923 (m170)
REVERT: E  517 LEU cc_start: 0.8599 (mm) cc_final: 0.8385 (mp)
REVERT: A   23 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7126 (mp0)
REVERT: A   26 LYS cc_start: 0.8195 (mttt) cc_final: 0.7868 (mmtt)
REVERT: A   29 LEU cc_start: 0.8478 (mt) cc_final: 0.8209 (mt)
REVERT: A   31 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7170 (tttp)
REVERT: A   40 PHE cc_start: 0.8624 (t80) cc_final: 0.8371 (t80)
REVERT: A   47 SER cc_start: 0.8791 (t) cc_final: 0.8387 (p)
REVERT: A   55 THR cc_start: 0.7905 (m) cc_final: 0.7347 (p)
REVERT: A   62 MET cc_start: 0.8199 (tmm) cc_final: 0.7316 (tmm)
REVERT: A  101 GLN cc_start: 0.7835 (tt0) cc_final: 0.7466 (tp40)
REVERT: A  121 ASN cc_start: 0.8872 (m-40) cc_final: 0.8561 (m110)
REVERT: A  123 MET cc_start: 0.8357 (ttt) cc_final: 0.7934 (mtt)
REVERT: A  126 ILE cc_start: 0.8883 (tp) cc_final: 0.8668 (tt)
REVERT: A  155 SER cc_start: 0.7353 (t) cc_final: 0.6900 (p)
REVERT: A  166 GLU cc_start: 0.7210 (tp30) cc_final: 0.6881 (tp30)
REVERT: A  168 TRP cc_start: 0.8340 (t-100) cc_final: 0.7946 (t-100)
REVERT: A  227 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7676 (tp30)
REVERT: A  249 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7126 (tmm)
REVERT: A  271 TRP cc_start: 0.5037 (t60) cc_final: 0.4204 (t60)
REVERT: A  299 ASP cc_start: 0.8212 (t0) cc_final: 0.7958 (t0)
REVERT: A  310 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7585 (mm-30)
REVERT: A  313 LYS cc_start: 0.7922 (mttt) cc_final: 0.7486 (ttmm)
REVERT: A  332 MET cc_start: 0.7788 (tmm) cc_final: 0.7548 (tmm)
REVERT: A  375 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7495 (mm-30)
REVERT: A  406 GLU cc_start: 0.7899 (tp30) cc_final: 0.7603 (tp30)
REVERT: A  465 LYS cc_start: 0.8772 (mttt) cc_final: 0.8337 (ttmt)
REVERT: A  472 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7268 (mm-40)
REVERT: A  473 TRP cc_start: 0.7635 (t-100) cc_final: 0.6645 (t-100)
REVERT: A  480 MET cc_start: 0.8706 (mmm) cc_final: 0.8289 (mmm)
REVERT: A  484 ILE cc_start: 0.8710 (mt) cc_final: 0.8431 (mt)
REVERT: A  499 ASP cc_start: 0.8467 (m-30) cc_final: 0.8196 (t0)
REVERT: A  518 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7540 (tmm-80)
REVERT: A  559 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7903 (ptm160)
REVERT: A  574 VAL cc_start: 0.9065 (m) cc_final: 0.8774 (p)
REVERT: A  582 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7119 (tpp80)
REVERT: A  603 PHE cc_start: 0.7205 (t80) cc_final: 0.6861 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 216
  average time/residue: 0.2473
  time to fit residues: 67.1478
Evaluate side-chains
  226 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  472 ILE
Chi-restraints excluded: chain E residue  483 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  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  375 GLU
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  579 MET
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 45 optimal weight:    0.0020
   chunk 36 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 72 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0270
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.2446

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

Flipped N/Q/H residues before XYZ refinement:
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 ASN
A 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.112005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096782 restraints weight = 11954.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100487 restraints weight = 5564.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.102837 restraints weight = 3140.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6618  Z= 0.137
  Angle     :  0.706  10.096   9000  Z= 0.347
  Chirality :  0.044   0.138    939
  Planarity :  0.004   0.045   1166
  Dihedral  :  4.785  49.272    861
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.67 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 28.45 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.30), residues: 787
  helix: -0.92 (0.26), residues: 373
  sheet: -1.39 (0.79), residues: 35
  loop : -0.45 (0.35), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 478 
 HIS   0.003   0.000   HIS A 378 
 PHE   0.024   0.002   PHE A 428 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.005   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  200)
  hydrogen bonds       : angle       4.45142 (  555)
  SS BOND              : bond        0.00330 (    7)
  SS BOND              : angle       2.06287 (   14)
  covalent geometry    : bond        0.00322 ( 6611)
  covalent geometry    : angle       0.70169 ( 8986)

*********************** 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
  231 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 205
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8069 (ttp80)
REVERT: E  422 ASN cc_start: 0.8123 (m110) cc_final: 0.7826 (m110)
REVERT: E  442 ASP cc_start: 0.8660 (t70) cc_final: 0.8179 (t0)
REVERT: E  494 SER cc_start: 0.8772 (m) cc_final: 0.8290 (p)
REVERT: E  505 HIS cc_start: 0.8175 (m170) cc_final: 0.7830 (m90)
REVERT: E  517 LEU cc_start: 0.8593 (mm) cc_final: 0.8393 (mp)
REVERT: A   29 LEU cc_start: 0.8398 (mt) cc_final: 0.8159 (mt)
REVERT: A   31 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7097 (tttp)
REVERT: A   40 PHE cc_start: 0.8579 (t80) cc_final: 0.8303 (t80)
REVERT: A   47 SER cc_start: 0.8762 (t) cc_final: 0.8370 (p)
REVERT: A   55 THR cc_start: 0.7920 (m) cc_final: 0.7355 (p)
REVERT: A   58 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8258 (t0)
REVERT: A   62 MET cc_start: 0.8220 (tmm) cc_final: 0.7342 (tmm)
REVERT: A   82 MET cc_start: 0.7692 (tpp) cc_final: 0.7456 (tpt)
REVERT: A  101 GLN cc_start: 0.7862 (tt0) cc_final: 0.7421 (tp40)
REVERT: A  121 ASN cc_start: 0.8932 (m-40) cc_final: 0.8563 (m110)
REVERT: A  123 MET cc_start: 0.8484 (ttt) cc_final: 0.8117 (ttp)
REVERT: A  126 ILE cc_start: 0.8817 (tp) cc_final: 0.8616 (tt)
REVERT: A  163 TRP cc_start: 0.7377 (t60) cc_final: 0.7147 (t60)
REVERT: A  166 GLU cc_start: 0.7128 (tp30) cc_final: 0.6820 (tp30)
REVERT: A  168 TRP cc_start: 0.8280 (t-100) cc_final: 0.7926 (t-100)
REVERT: A  204 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7931 (mtm180)
REVERT: A  227 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7695 (tp30)
REVERT: A  249 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7099 (tmm)
REVERT: A  267 LEU cc_start: 0.8533 (mp) cc_final: 0.8274 (mm)
REVERT: A  271 TRP cc_start: 0.5071 (t60) cc_final: 0.4234 (t60)
REVERT: A  299 ASP cc_start: 0.8278 (t0) cc_final: 0.8043 (t0)
REVERT: A  310 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: A  313 LYS cc_start: 0.7543 (mttt) cc_final: 0.7302 (ttpt)
REVERT: A  332 MET cc_start: 0.7740 (tmm) cc_final: 0.7520 (tmm)
REVERT: A  353 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7660 (mtpt)
REVERT: A  375 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7341 (mm-30)
REVERT: A  465 LYS cc_start: 0.8763 (mttt) cc_final: 0.8321 (ttmt)
REVERT: A  473 TRP cc_start: 0.7467 (t-100) cc_final: 0.7173 (t-100)
REVERT: A  475 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7791 (tptp)
REVERT: A  480 MET cc_start: 0.8750 (mmm) cc_final: 0.8413 (mmm)
REVERT: A  484 ILE cc_start: 0.8726 (mt) cc_final: 0.8232 (mm)
REVERT: A  518 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7459 (tmm-80)
REVERT: A  559 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7911 (ptm160)
REVERT: A  574 VAL cc_start: 0.9079 (m) cc_final: 0.8813 (p)
REVERT: A  582 ARG cc_start: 0.7499 (tpp80) cc_final: 0.7076 (tpp80)
REVERT: A  600 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8429 (mmmm)
REVERT: A  603 PHE cc_start: 0.7247 (t80) cc_final: 0.6895 (t80)
  outliers start: 26
  outliers final: 17
  residues processed: 217
  average time/residue: 0.2340
  time to fit residues: 63.1619
Evaluate side-chains
  223 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  472 ILE
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   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  375 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  579 MET
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 22 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.106737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.091827 restraints weight = 12378.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.095401 restraints weight = 5754.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.097641 restraints weight = 3257.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.5207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6618  Z= 0.282
  Angle     :  0.801  11.423   9000  Z= 0.399
  Chirality :  0.050   0.171    939
  Planarity :  0.004   0.057   1166
  Dihedral  :  5.305  48.816    861
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.32 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.30 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.30), residues: 787
  helix: -1.04 (0.26), residues: 373
  sheet: -2.04 (0.68), residues: 47
  loop : -0.37 (0.35), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 436 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.028   0.002   PHE A 315 
 TYR   0.024   0.002   TYR A 158 
 ARG   0.005   0.001   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  200)
  hydrogen bonds       : angle       4.84425 (  555)
  SS BOND              : bond        0.00417 (    7)
  SS BOND              : angle       2.92160 (   14)
  covalent geometry    : bond        0.00630 ( 6611)
  covalent geometry    : angle       0.79304 ( 8986)

*********************** 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
  230 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 201
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7901 (ttp80)
REVERT: E  422 ASN cc_start: 0.8243 (m110) cc_final: 0.7905 (m-40)
REVERT: E  442 ASP cc_start: 0.8697 (t70) cc_final: 0.8144 (t0)
REVERT: E  494 SER cc_start: 0.8899 (m) cc_final: 0.8368 (p)
REVERT: E  505 HIS cc_start: 0.8388 (m170) cc_final: 0.7920 (m90)
REVERT: E  517 LEU cc_start: 0.8700 (mm) cc_final: 0.8427 (mp)
REVERT: A   31 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7220 (tttp)
REVERT: A   40 PHE cc_start: 0.8646 (t80) cc_final: 0.8368 (t80)
REVERT: A   47 SER cc_start: 0.8770 (t) cc_final: 0.8443 (p)
REVERT: A   55 THR cc_start: 0.8028 (m) cc_final: 0.7451 (p)
REVERT: A   62 MET cc_start: 0.8265 (tmm) cc_final: 0.7398 (tmm)
REVERT: A  101 GLN cc_start: 0.7892 (tt0) cc_final: 0.7633 (tt0)
REVERT: A  123 MET cc_start: 0.8521 (ttt) cc_final: 0.8314 (ttp)
REVERT: A  126 ILE cc_start: 0.8935 (tp) cc_final: 0.8675 (tt)
REVERT: A  163 TRP cc_start: 0.7470 (t60) cc_final: 0.7229 (t60)
REVERT: A  166 GLU cc_start: 0.7353 (tp30) cc_final: 0.6955 (tp30)
REVERT: A  182 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7120 (mt-10)
REVERT: A  227 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7691 (tp30)
REVERT: A  249 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7298 (tmm)
REVERT: A  271 TRP cc_start: 0.5139 (t60) cc_final: 0.4018 (t60)
REVERT: A  299 ASP cc_start: 0.8337 (t0) cc_final: 0.8119 (t0)
REVERT: A  312 GLU cc_start: 0.7471 (tp30) cc_final: 0.7129 (tp30)
REVERT: A  315 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7580 (t80)
REVERT: A  332 MET cc_start: 0.7782 (tmm) cc_final: 0.7580 (tmm)
REVERT: A  353 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7744 (mmmt)
REVERT: A  375 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7406 (mm-30)
REVERT: A  402 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: A  465 LYS cc_start: 0.8850 (mttt) cc_final: 0.8389 (ttmt)
REVERT: A  473 TRP cc_start: 0.7368 (t-100) cc_final: 0.6476 (t-100)
REVERT: A  475 LYS cc_start: 0.8448 (tmtt) cc_final: 0.8124 (tptp)
REVERT: A  480 MET cc_start: 0.8801 (mmm) cc_final: 0.8497 (mmm)
REVERT: A  484 ILE cc_start: 0.8749 (mt) cc_final: 0.8455 (mm)
REVERT: A  559 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7992 (ptm160)
REVERT: A  574 VAL cc_start: 0.9044 (m) cc_final: 0.8775 (p)
REVERT: A  582 ARG cc_start: 0.7591 (tpp80) cc_final: 0.7148 (tpp80)
REVERT: A  603 PHE cc_start: 0.7302 (t80) cc_final: 0.6928 (t80)
  outliers start: 29
  outliers final: 16
  residues processed: 216
  average time/residue: 0.2270
  time to fit residues: 61.6988
Evaluate side-chains
  221 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  177 ARG
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  315 PHE
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  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
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  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  579 MET
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 13 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0470
   chunk 12 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0670
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.2216

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.111876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.096687 restraints weight = 12307.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.100380 restraints weight = 5703.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102730 restraints weight = 3202.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.5419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6618  Z= 0.144
  Angle     :  0.755  11.672   9000  Z= 0.372
  Chirality :  0.045   0.149    939
  Planarity :  0.004   0.039   1166
  Dihedral  :  5.009  46.147    861
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.16 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 30.89 %
    Favored  : 66.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.30), residues: 787
  helix: -0.76 (0.27), residues: 367
  sheet: -1.95 (0.70), residues: 47
  loop : -0.36 (0.35), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.020   0.002   PHE A 315 
 TYR   0.020   0.002   TYR E 501 
 ARG   0.006   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  200)
  hydrogen bonds       : angle       4.52561 (  555)
  SS BOND              : bond        0.00209 (    7)
  SS BOND              : angle       2.31198 (   14)
  covalent geometry    : bond        0.00338 ( 6611)
  covalent geometry    : angle       0.75007 ( 8986)

********************** 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
  223 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 202
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7782 (ttp80)
REVERT: E  422 ASN cc_start: 0.8093 (m110) cc_final: 0.7860 (m110)
REVERT: E  442 ASP cc_start: 0.8671 (t70) cc_final: 0.8164 (t0)
REVERT: E  494 SER cc_start: 0.8809 (m) cc_final: 0.8381 (p)
REVERT: E  505 HIS cc_start: 0.8115 (m170) cc_final: 0.7763 (m170)
REVERT: A   26 LYS cc_start: 0.8238 (mttt) cc_final: 0.7876 (mmmm)
REVERT: A   31 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7070 (tttp)
REVERT: A   40 PHE cc_start: 0.8578 (t80) cc_final: 0.8243 (t80)
REVERT: A   47 SER cc_start: 0.8784 (t) cc_final: 0.8393 (p)
REVERT: A   55 THR cc_start: 0.7993 (m) cc_final: 0.7416 (p)
REVERT: A   62 MET cc_start: 0.8290 (tmm) cc_final: 0.7435 (tmm)
REVERT: A  101 GLN cc_start: 0.7827 (tt0) cc_final: 0.7351 (tp40)
REVERT: A  121 ASN cc_start: 0.8967 (m-40) cc_final: 0.8582 (m110)
REVERT: A  124 SER cc_start: 0.8573 (m) cc_final: 0.8336 (p)
REVERT: A  126 ILE cc_start: 0.8843 (tp) cc_final: 0.8622 (tt)
REVERT: A  163 TRP cc_start: 0.7335 (t60) cc_final: 0.7117 (t60)
REVERT: A  166 GLU cc_start: 0.7216 (tp30) cc_final: 0.6864 (tp30)
REVERT: A  182 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6740 (mt-10)
REVERT: A  227 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7662 (tp30)
REVERT: A  271 TRP cc_start: 0.5051 (t60) cc_final: 0.4100 (t60)
REVERT: A  299 ASP cc_start: 0.8311 (t0) cc_final: 0.8044 (t0)
REVERT: A  312 GLU cc_start: 0.7370 (tp30) cc_final: 0.7109 (tp30)
REVERT: A  323 MET cc_start: 0.7662 (mtp) cc_final: 0.7301 (mmm)
REVERT: A  332 MET cc_start: 0.7801 (tmm) cc_final: 0.7522 (tmm)
REVERT: A  353 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7561 (mtpp)
REVERT: A  375 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7108 (mm-30)
REVERT: A  406 GLU cc_start: 0.7983 (tp30) cc_final: 0.7777 (tp30)
REVERT: A  465 LYS cc_start: 0.8687 (mttt) cc_final: 0.8261 (ttmt)
REVERT: A  473 TRP cc_start: 0.7151 (t-100) cc_final: 0.6848 (t-100)
REVERT: A  475 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7729 (tptp)
REVERT: A  476 LYS cc_start: 0.7652 (mtpt) cc_final: 0.7448 (mtpt)
REVERT: A  480 MET cc_start: 0.8654 (mmm) cc_final: 0.8437 (mmm)
REVERT: A  484 ILE cc_start: 0.8805 (mt) cc_final: 0.8366 (mt)
REVERT: A  559 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7923 (ptm160)
REVERT: A  574 VAL cc_start: 0.9051 (m) cc_final: 0.8811 (p)
REVERT: A  577 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8336 (ptpp)
REVERT: A  582 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7096 (tpp80)
REVERT: A  600 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8442 (mmmm)
REVERT: A  603 PHE cc_start: 0.7294 (t80) cc_final: 0.6942 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 214
  average time/residue: 0.2360
  time to fit residues: 63.6010
Evaluate side-chains
  218 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 201
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   95 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  203 TRP
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  407 ILE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  579 MET
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 70 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    0.1980
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN
** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.108596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.093378 restraints weight = 12487.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.097029 restraints weight = 5771.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099352 restraints weight = 3240.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6618  Z= 0.226
  Angle     :  0.793  10.731   9000  Z= 0.394
  Chirality :  0.048   0.145    939
  Planarity :  0.004   0.040   1166
  Dihedral  :  5.186  44.657    861
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 30.46 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.30), residues: 787
  helix: -0.84 (0.26), residues: 369
  sheet: -2.03 (0.65), residues: 51
  loop : -0.36 (0.35), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 168 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.027   0.002   PHE A 428 
 TYR   0.022   0.002   TYR A 158 
 ARG   0.007   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04368 (  200)
  hydrogen bonds       : angle       4.71463 (  555)
  SS BOND              : bond        0.00310 (    7)
  SS BOND              : angle       2.69565 (   14)
  covalent geometry    : bond        0.00515 ( 6611)
  covalent geometry    : angle       0.78687 ( 8986)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3810.98 seconds
wall clock time: 67 minutes 40.10 seconds (4060.10 seconds total)