Starting phenix.real_space_refine
on Tue Feb 13 13:28:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/02_2024/7wk6_32560.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/02_2024/7wk6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/02_2024/7wk6_32560.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/02_2024/7wk6_32560.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/02_2024/7wk6_32560.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/02_2024/7wk6_32560.pdb"
  }
  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
    Residue "E ASP  442": "OD1" <-> "OD2"
    Residue "E ARG  493": "NH1" <-> "NH2"
    Residue "E ARG  498": "NH1" <-> "NH2"
    Residue "E GLU  516": "OE1" <-> "OE2"
    Residue "A GLU   22": "OE1" <-> "OE2"
    Residue "A GLU   23": "OE1" <-> "OE2"
    Residue "A GLU   35": "OE1" <-> "OE2"
    Residue "A GLU   56": "OE1" <-> "OE2"
    Residue "A GLU   87": "OE1" <-> "OE2"
    Residue "A GLU  166": "OE1" <-> "OE2"
    Residue "A GLU  171": "OE1" <-> "OE2"
    Residue "A GLU  182": "OE1" <-> "OE2"
    Residue "A GLU  189": "OE1" <-> "OE2"
    Residue "A GLU  232": "OE1" <-> "OE2"
    Residue "A GLU  238": "OE1" <-> "OE2"
    Residue "A ARG  245": "NH1" <-> "NH2"
    Residue "A GLU  398": "OE1" <-> "OE2"
    Residue "A GLU  402": "OE1" <-> "OE2"
    Residue "A GLU  433": "OE1" <-> "OE2"
    Residue "A GLU  435": "OE1" <-> "OE2"
    Residue "A GLU  467": "OE1" <-> "OE2"
    Residue "A GLU  483": "OE1" <-> "OE2"
    Residue "A GLU  495": "OE1" <-> "OE2"
    Residue "A GLU  527": "OE1" <-> "OE2"
    Residue "A GLU  536": "OE1" <-> "OE2"
    Residue "A GLU  564": "OE1" <-> "OE2"
    Residue "A GLU  571": "OE1" <-> "OE2"
    Residue "A GLU  589": "OE1" <-> "OE2"
    Residue "A TYR  613": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.93, per 1000 atoms: 0.61
  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  - 3.50
        Amino acid           : False - 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: 2.21
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.63

  Time building geometry restraints manager: 2.44 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:
       90.89 -    99.58: 1
       99.58 -   108.26: 380
      108.26 -   116.94: 3998
      116.94 -   125.63: 4455
      125.63 -   134.31: 152
  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 2.440
  nonbonded pdb=" O   SER A 254 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.333 2.440
  nonbonded pdb=" OD1 ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.337 2.440
  nonbonded pdb=" O   ASN A 121 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.351 2.440
  nonbonded pdb=" OG1 THR E 500 "
            pdb=" OH  TYR A  41 "
     model   vdw
     2.371 2.440
  ... (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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          9.800
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     20.380
  Find NCS groups from input model:        0.160
  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:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.760
-------------------------------------------------------------------------------
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   6611  Z= 0.485
  Angle     :  1.068  16.306   8986  Z= 0.647
  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 

*********************** 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 fitting.
    rotamer outliers: 4
    poor density    : 250
  time to evaluate  : 0.774 
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: 0.2355
  time to fit residues: 74.2594
Evaluate side-chains
  227 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 224
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 59 optimal weight:    0.0000
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0770
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0070
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.1960

-------------------------------------------------------------------------------
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  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6611  Z= 0.173
  Angle     :  0.610   8.949   8986  Z= 0.316
  Chirality :  0.043   0.126    939
  Planarity :  0.004   0.037   1166
  Dihedral  :  5.302  63.517    864
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.96 %
    Favored  : 79.60 %
  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: -3.61 (0.26), residues: 787
  helix: -3.18 (0.20), residues: 352
  sheet: -1.38 (0.92), residues: 33
  loop : -1.62 (0.29), residues: 402

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   0.010   0.001   PHE A 327 
 TYR   0.017   0.001   TYR E 489 
 ARG   0.003   0.000   ARG E 493 

*********************** 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
  237 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 220
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  422 ASN cc_start: 0.8033 (m110) cc_final: 0.7650 (m-40)
REVERT: E  442 ASP cc_start: 0.8682 (t70) cc_final: 0.8304 (t0)
REVERT: E  465 GLU cc_start: 0.7942 (tt0) cc_final: 0.7690 (tt0)
REVERT: E  467 ASP cc_start: 0.7990 (p0) cc_final: 0.7525 (p0)
REVERT: E  494 SER cc_start: 0.8837 (m) cc_final: 0.8439 (p)
REVERT: A   26 LYS cc_start: 0.8121 (mttt) cc_final: 0.7804 (mmmm)
REVERT: A   42 GLN cc_start: 0.8243 (tt0) cc_final: 0.7994 (tt0)
REVERT: A   47 SER cc_start: 0.8651 (t) cc_final: 0.8364 (t)
REVERT: A   55 THR cc_start: 0.7727 (m) cc_final: 0.7030 (p)
REVERT: A   62 MET cc_start: 0.7941 (tmm) cc_final: 0.7229 (tmm)
REVERT: A  101 GLN cc_start: 0.7943 (tt0) cc_final: 0.7725 (mt0)
REVERT: A  105 SER cc_start: 0.8346 (p) cc_final: 0.7938 (t)
REVERT: A  110 GLU cc_start: 0.7244 (tp30) cc_final: 0.6955 (tp30)
REVERT: A  126 ILE cc_start: 0.8937 (tp) cc_final: 0.8637 (tt)
REVERT: A  142 LEU cc_start: 0.7842 (mt) cc_final: 0.7634 (mt)
REVERT: A  144 LEU cc_start: 0.8274 (tp) cc_final: 0.7797 (tp)
REVERT: A  157 ASP cc_start: 0.7923 (m-30) cc_final: 0.7627 (t70)
REVERT: A  158 TYR cc_start: 0.7280 (t80) cc_final: 0.6777 (t80)
REVERT: A  168 TRP cc_start: 0.8250 (t-100) cc_final: 0.7835 (t-100)
REVERT: A  182 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6889 (tm-30)
REVERT: A  186 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7998 (mp)
REVERT: A  227 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: A  265 HIS cc_start: 0.8900 (p-80) cc_final: 0.8600 (p-80)
REVERT: A  267 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8347 (mm)
REVERT: A  271 TRP cc_start: 0.4977 (t60) cc_final: 0.4444 (t60)
REVERT: A  313 LYS cc_start: 0.8133 (mttt) cc_final: 0.7643 (mtpt)
REVERT: A  325 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7300 (tp-100)
REVERT: A  332 MET cc_start: 0.8059 (ttp) cc_final: 0.7574 (tmm)
REVERT: A  353 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7775 (mttm)
REVERT: A  363 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8342 (mppt)
REVERT: A  368 ASP cc_start: 0.8180 (t0) cc_final: 0.7217 (t0)
REVERT: A  429 GLN cc_start: 0.7339 (tp40) cc_final: 0.7055 (tp40)
REVERT: A  465 LYS cc_start: 0.8660 (mttt) cc_final: 0.8350 (ttmt)
REVERT: A  472 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7466 (mm-40)
REVERT: A  475 LYS cc_start: 0.8299 (tppt) cc_final: 0.8042 (tmtt)
REVERT: A  476 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7525 (mtpt)
REVERT: A  499 ASP cc_start: 0.7870 (m-30) cc_final: 0.7081 (t0)
REVERT: A  500 PRO cc_start: 0.8551 (Cg_endo) cc_final: 0.8136 (Cg_exo)
REVERT: A  504 PHE cc_start: 0.7908 (t80) cc_final: 0.7678 (t80)
REVERT: A  531 GLN cc_start: 0.8389 (tp-100) cc_final: 0.7951 (tp-100)
REVERT: A  574 VAL cc_start: 0.8978 (m) cc_final: 0.8740 (p)
REVERT: A  582 ARG cc_start: 0.7429 (tpp80) cc_final: 0.6961 (mpp80)
REVERT: A  603 PHE cc_start: 0.6968 (t80) cc_final: 0.6606 (t80)
  outliers start: 17
  outliers final: 6
  residues processed: 230
  average time/residue: 0.2313
  time to fit residues: 67.7900
Evaluate side-chains
  210 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 202
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  111 ASP
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0980
   chunk 63 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6611  Z= 0.305
  Angle     :  0.678   9.014   8986  Z= 0.343
  Chirality :  0.046   0.126    939
  Planarity :  0.004   0.043   1166
  Dihedral  :  5.072  53.266    861
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 20.26 %
    Favored  : 75.29 %
  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: -2.84 (0.27), residues: 787
  helix: -2.47 (0.23), residues: 356
  sheet: -1.44 (0.84), residues: 35
  loop : -1.21 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 436 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.029   0.002   PHE A 428 
 TYR   0.015   0.002   TYR E 489 
 ARG   0.006   0.001   ARG A 219 

*********************** 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
  242 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: E  335 LEU cc_start: 0.8388 (tp) cc_final: 0.8162 (tp)
REVERT: E  422 ASN cc_start: 0.8127 (m110) cc_final: 0.7843 (m-40)
REVERT: E  442 ASP cc_start: 0.8764 (t70) cc_final: 0.8268 (t0)
REVERT: E  467 ASP cc_start: 0.8108 (p0) cc_final: 0.7590 (p0)
REVERT: E  473 TYR cc_start: 0.7724 (t80) cc_final: 0.7346 (t80)
REVERT: E  494 SER cc_start: 0.8912 (m) cc_final: 0.8366 (p)
REVERT: E  517 LEU cc_start: 0.8733 (mm) cc_final: 0.8359 (mp)
REVERT: A   26 LYS cc_start: 0.8224 (mttt) cc_final: 0.7954 (mmtt)
REVERT: A   40 PHE cc_start: 0.8682 (t80) cc_final: 0.8313 (t80)
REVERT: A   47 SER cc_start: 0.8768 (t) cc_final: 0.8504 (t)
REVERT: A   55 THR cc_start: 0.7775 (m) cc_final: 0.7077 (p)
REVERT: A   62 MET cc_start: 0.8074 (tmm) cc_final: 0.7263 (tmm)
REVERT: A  101 GLN cc_start: 0.8078 (tt0) cc_final: 0.7841 (tt0)
REVERT: A  105 SER cc_start: 0.8362 (p) cc_final: 0.8015 (t)
REVERT: A  110 GLU cc_start: 0.7585 (tp30) cc_final: 0.7000 (tp30)
REVERT: A  126 ILE cc_start: 0.9048 (tp) cc_final: 0.8645 (tt)
REVERT: A  142 LEU cc_start: 0.8008 (mt) cc_final: 0.7768 (mt)
REVERT: A  144 LEU cc_start: 0.8497 (tp) cc_final: 0.7917 (tp)
REVERT: A  157 ASP cc_start: 0.8014 (m-30) cc_final: 0.7643 (t0)
REVERT: A  158 TYR cc_start: 0.7496 (t80) cc_final: 0.7132 (t80)
REVERT: A  168 TRP cc_start: 0.8327 (t-100) cc_final: 0.7833 (t-100)
REVERT: A  224 GLU cc_start: 0.7915 (tp30) cc_final: 0.7615 (tp30)
REVERT: A  227 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7681 (tp30)
REVERT: A  265 HIS cc_start: 0.9020 (p-80) cc_final: 0.8749 (p-80)
REVERT: A  267 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8358 (mt)
REVERT: A  271 TRP cc_start: 0.5045 (t60) cc_final: 0.4309 (t60)
REVERT: A  277 ASN cc_start: 0.8590 (m-40) cc_final: 0.8384 (m110)
REVERT: A  313 LYS cc_start: 0.8045 (mttt) cc_final: 0.7781 (mtpt)
REVERT: A  330 ASN cc_start: 0.8333 (m-40) cc_final: 0.8088 (p0)
REVERT: A  363 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8226 (mppt)
REVERT: A  368 ASP cc_start: 0.8042 (t0) cc_final: 0.7818 (t0)
REVERT: A  406 GLU cc_start: 0.7945 (tp30) cc_final: 0.7646 (tp30)
REVERT: A  429 GLN cc_start: 0.7480 (tp40) cc_final: 0.7157 (tp40)
REVERT: A  465 LYS cc_start: 0.8853 (mttt) cc_final: 0.8355 (ttmt)
REVERT: A  475 LYS cc_start: 0.8381 (tppt) cc_final: 0.8103 (tmtt)
REVERT: A  504 PHE cc_start: 0.8151 (t80) cc_final: 0.7776 (t80)
REVERT: A  514 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7912 (mtm110)
REVERT: A  559 ARG cc_start: 0.8153 (ptt180) cc_final: 0.7876 (ptm160)
REVERT: A  603 PHE cc_start: 0.7205 (t80) cc_final: 0.6828 (t80)
  outliers start: 31
  outliers final: 16
  residues processed: 222
  average time/residue: 0.2432
  time to fit residues: 67.9846
Evaluate side-chains
  226 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 209
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain E residue  503 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0000
   chunk 71 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 62 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  81 GLN
A 103 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6611  Z= 0.233
  Angle     :  0.643  10.254   8986  Z= 0.322
  Chirality :  0.044   0.139    939
  Planarity :  0.004   0.033   1166
  Dihedral  :  4.778  48.589    861
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.42 %
    Favored  : 72.56 %
  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: -2.39 (0.28), residues: 787
  helix: -2.01 (0.24), residues: 358
  sheet: -1.47 (0.83), residues: 37
  loop : -1.02 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 436 
 HIS   0.003   0.001   HIS E 505 
 PHE   0.017   0.001   PHE A 400 
 TYR   0.025   0.002   TYR A 158 
 ARG   0.006   0.001   ARG E 357 

*********************** 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
  249 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7627 (ttp80)
REVERT: E  442 ASP cc_start: 0.8747 (t70) cc_final: 0.8176 (t0)
REVERT: E  467 ASP cc_start: 0.8168 (p0) cc_final: 0.7662 (p0)
REVERT: E  473 TYR cc_start: 0.7764 (t80) cc_final: 0.7403 (t80)
REVERT: E  494 SER cc_start: 0.8885 (m) cc_final: 0.8394 (p)
REVERT: E  505 HIS cc_start: 0.8365 (m170) cc_final: 0.7943 (m170)
REVERT: E  517 LEU cc_start: 0.8786 (mm) cc_final: 0.8413 (mp)
REVERT: A   26 LYS cc_start: 0.8237 (mttt) cc_final: 0.7908 (mmtt)
REVERT: A   40 PHE cc_start: 0.8584 (t80) cc_final: 0.8321 (t80)
REVERT: A   47 SER cc_start: 0.8768 (t) cc_final: 0.8510 (t)
REVERT: A   55 THR cc_start: 0.7819 (m) cc_final: 0.7214 (p)
REVERT: A   57 GLU cc_start: 0.8385 (pp20) cc_final: 0.8167 (pp20)
REVERT: A   62 MET cc_start: 0.8135 (tmm) cc_final: 0.7308 (tmm)
REVERT: A   75 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A  101 GLN cc_start: 0.8162 (tt0) cc_final: 0.7888 (tt0)
REVERT: A  121 ASN cc_start: 0.8619 (m-40) cc_final: 0.8362 (m-40)
REVERT: A  123 MET cc_start: 0.8315 (ttt) cc_final: 0.7791 (ttp)
REVERT: A  126 ILE cc_start: 0.8883 (tp) cc_final: 0.8616 (tt)
REVERT: A  144 LEU cc_start: 0.8421 (tp) cc_final: 0.7993 (tp)
REVERT: A  157 ASP cc_start: 0.7958 (m-30) cc_final: 0.7649 (t0)
REVERT: A  160 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6848 (tm-30)
REVERT: A  161 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8522 (mtp180)
REVERT: A  163 TRP cc_start: 0.7875 (t60) cc_final: 0.7593 (t60)
REVERT: A  168 TRP cc_start: 0.8345 (t-100) cc_final: 0.7819 (t-100)
REVERT: A  182 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6974 (tm-30)
REVERT: A  189 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7221 (tp30)
REVERT: A  227 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7662 (tp30)
REVERT: A  265 HIS cc_start: 0.8988 (p-80) cc_final: 0.8634 (p-80)
REVERT: A  267 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8316 (mt)
REVERT: A  271 TRP cc_start: 0.5063 (t60) cc_final: 0.4180 (t60)
REVERT: A  313 LYS cc_start: 0.8080 (mttt) cc_final: 0.7783 (ttmm)
REVERT: A  330 ASN cc_start: 0.8359 (m-40) cc_final: 0.8001 (p0)
REVERT: A  332 MET cc_start: 0.7813 (tmm) cc_final: 0.7463 (tmm)
REVERT: A  363 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8193 (mppt)
REVERT: A  406 GLU cc_start: 0.7934 (tp30) cc_final: 0.7621 (tp30)
REVERT: A  429 GLN cc_start: 0.7448 (tp40) cc_final: 0.7074 (tp40)
REVERT: A  465 LYS cc_start: 0.8845 (mttt) cc_final: 0.8301 (ttmt)
REVERT: A  472 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7675 (mm-40)
REVERT: A  475 LYS cc_start: 0.8297 (tppt) cc_final: 0.8049 (tmtt)
REVERT: A  504 PHE cc_start: 0.8110 (t80) cc_final: 0.7754 (t80)
REVERT: A  557 MET cc_start: 0.7924 (tmm) cc_final: 0.7656 (tmm)
REVERT: A  559 ARG cc_start: 0.8150 (ptt180) cc_final: 0.7817 (ptm160)
REVERT: A  577 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8614 (ptpp)
REVERT: A  582 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7104 (tpp80)
REVERT: A  603 PHE cc_start: 0.7229 (t80) cc_final: 0.6846 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 230
  average time/residue: 0.2331
  time to fit residues: 67.4385
Evaluate side-chains
  225 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  387 LEU
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain A residue   20 THR
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  189 GLU
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  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
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0870
   chunk 52 optimal weight:    0.4980
   chunk 0 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0670
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
A 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6611  Z= 0.208
  Angle     :  0.641  11.933   8986  Z= 0.319
  Chirality :  0.044   0.131    939
  Planarity :  0.004   0.042   1166
  Dihedral  :  4.746  43.658    861
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.18 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.43 %
    Favored  : 70.26 %
  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: -2.00 (0.29), residues: 787
  helix: -1.63 (0.25), residues: 366
  sheet: -1.86 (0.70), residues: 48
  loop : -0.73 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.015   0.001   PHE A 327 
 TYR   0.034   0.002   TYR A 158 
 ARG   0.004   0.000   ARG E 493 

*********************** 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
  236 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 206
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  403 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7602 (ttp80)
REVERT: E  417 ASN cc_start: 0.7929 (t0) cc_final: 0.7728 (t0)
REVERT: E  421 TYR cc_start: 0.8272 (m-80) cc_final: 0.7991 (m-80)
REVERT: E  422 ASN cc_start: 0.8198 (m110) cc_final: 0.7777 (m-40)
REVERT: E  442 ASP cc_start: 0.8747 (t70) cc_final: 0.8175 (t0)
REVERT: E  467 ASP cc_start: 0.8281 (p0) cc_final: 0.7757 (p0)
REVERT: E  494 SER cc_start: 0.8855 (m) cc_final: 0.8462 (p)
REVERT: E  505 HIS cc_start: 0.8326 (m170) cc_final: 0.7799 (m90)
REVERT: E  517 LEU cc_start: 0.8731 (mm) cc_final: 0.8452 (mp)
REVERT: A   26 LYS cc_start: 0.8267 (mttt) cc_final: 0.7942 (mmtt)
REVERT: A   40 PHE cc_start: 0.8568 (t80) cc_final: 0.8293 (t80)
REVERT: A   47 SER cc_start: 0.8739 (t) cc_final: 0.8470 (t)
REVERT: A   55 THR cc_start: 0.7810 (m) cc_final: 0.7177 (p)
REVERT: A   62 MET cc_start: 0.8148 (tmm) cc_final: 0.7298 (tmm)
REVERT: A  121 ASN cc_start: 0.8695 (m-40) cc_final: 0.8464 (m-40)
REVERT: A  123 MET cc_start: 0.8418 (ttt) cc_final: 0.7836 (ttp)
REVERT: A  126 ILE cc_start: 0.8859 (tp) cc_final: 0.8610 (tt)
REVERT: A  144 LEU cc_start: 0.8391 (tp) cc_final: 0.7916 (tp)
REVERT: A  157 ASP cc_start: 0.7943 (m-30) cc_final: 0.7660 (t0)
REVERT: A  160 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6968 (tm-30)
REVERT: A  163 TRP cc_start: 0.7710 (t60) cc_final: 0.7494 (t60)
REVERT: A  166 GLU cc_start: 0.7122 (tp30) cc_final: 0.6753 (tp30)
REVERT: A  168 TRP cc_start: 0.8301 (t-100) cc_final: 0.7698 (t-100)
REVERT: A  227 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7631 (tp30)
REVERT: A  249 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6919 (tmm)
REVERT: A  267 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (mt)
REVERT: A  271 TRP cc_start: 0.5028 (t60) cc_final: 0.4175 (t60)
REVERT: A  307 ILE cc_start: 0.8396 (tp) cc_final: 0.8184 (tt)
REVERT: A  310 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7348 (mm-30)
REVERT: A  313 LYS cc_start: 0.8009 (mttt) cc_final: 0.7671 (ttmm)
REVERT: A  330 ASN cc_start: 0.8310 (m-40) cc_final: 0.7975 (p0)
REVERT: A  353 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7266 (mttp)
REVERT: A  375 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7176 (mm-30)
REVERT: A  406 GLU cc_start: 0.7955 (tp30) cc_final: 0.7622 (tp30)
REVERT: A  429 GLN cc_start: 0.7356 (tp40) cc_final: 0.6962 (tp40)
REVERT: A  465 LYS cc_start: 0.8805 (mttt) cc_final: 0.8319 (ttmt)
REVERT: A  472 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7502 (mm-40)
REVERT: A  473 TRP cc_start: 0.7631 (t-100) cc_final: 0.6682 (t-100)
REVERT: A  475 LYS cc_start: 0.8329 (tppt) cc_final: 0.8064 (tmtt)
REVERT: A  504 PHE cc_start: 0.8115 (t80) cc_final: 0.7685 (t80)
REVERT: A  518 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7488 (tmm-80)
REVERT: A  557 MET cc_start: 0.7937 (tmm) cc_final: 0.7692 (tmm)
REVERT: A  559 ARG cc_start: 0.8153 (ptt180) cc_final: 0.7825 (ptm160)
REVERT: A  564 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7740 (mm-30)
REVERT: A  582 ARG cc_start: 0.7506 (tpp80) cc_final: 0.7057 (tpp80)
REVERT: A  603 PHE cc_start: 0.7237 (t80) cc_final: 0.6851 (t80)
  outliers start: 30
  outliers final: 19
  residues processed: 216
  average time/residue: 0.2483
  time to fit residues: 67.1895
Evaluate side-chains
  223 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  387 LEU
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  472 ILE
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 34 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0670
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6611  Z= 0.272
  Angle     :  0.667  10.924   8986  Z= 0.331
  Chirality :  0.046   0.137    939
  Planarity :  0.004   0.040   1166
  Dihedral  :  4.774  42.173    861
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.01 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z (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: -1.74 (0.30), residues: 787
  helix: -1.39 (0.26), residues: 364
  sheet: -1.81 (0.70), residues: 48
  loop : -0.61 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 436 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.017   0.002   PHE A 356 
 TYR   0.014   0.001   TYR A 180 
 ARG   0.004   0.000   ARG E 493 

*********************** 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
  240 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 208
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7825 (mtp85)
REVERT: E  403 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7656 (ttp80)
REVERT: E  421 TYR cc_start: 0.8297 (m-80) cc_final: 0.8021 (m-80)
REVERT: E  422 ASN cc_start: 0.8154 (m110) cc_final: 0.7726 (m-40)
REVERT: E  442 ASP cc_start: 0.8711 (t70) cc_final: 0.8185 (t0)
REVERT: E  467 ASP cc_start: 0.8318 (p0) cc_final: 0.7730 (p0)
REVERT: E  473 TYR cc_start: 0.7639 (t80) cc_final: 0.7163 (t80)
REVERT: E  494 SER cc_start: 0.8901 (m) cc_final: 0.8434 (p)
REVERT: E  505 HIS cc_start: 0.8366 (m170) cc_final: 0.7905 (m170)
REVERT: A   26 LYS cc_start: 0.8289 (mttt) cc_final: 0.7967 (mmtt)
REVERT: A   31 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7189 (tttp)
REVERT: A   40 PHE cc_start: 0.8566 (t80) cc_final: 0.8307 (t80)
REVERT: A   47 SER cc_start: 0.8742 (t) cc_final: 0.8483 (t)
REVERT: A   55 THR cc_start: 0.7876 (m) cc_final: 0.7259 (p)
REVERT: A   62 MET cc_start: 0.8201 (tmm) cc_final: 0.7308 (tmm)
REVERT: A   75 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7648 (tm-30)
REVERT: A  101 GLN cc_start: 0.8215 (tt0) cc_final: 0.7943 (tt0)
REVERT: A  110 GLU cc_start: 0.7034 (tp30) cc_final: 0.6758 (tp30)
REVERT: A  121 ASN cc_start: 0.8841 (m-40) cc_final: 0.8588 (m-40)
REVERT: A  123 MET cc_start: 0.8546 (ttt) cc_final: 0.8048 (ttp)
REVERT: A  126 ILE cc_start: 0.8900 (tp) cc_final: 0.8636 (tt)
REVERT: A  144 LEU cc_start: 0.8360 (tp) cc_final: 0.7935 (tp)
REVERT: A  157 ASP cc_start: 0.7972 (m-30) cc_final: 0.7615 (t0)
REVERT: A  158 TYR cc_start: 0.6458 (t80) cc_final: 0.6066 (t80)
REVERT: A  160 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7076 (tm-30)
REVERT: A  166 GLU cc_start: 0.7250 (tp30) cc_final: 0.6869 (tp30)
REVERT: A  168 TRP cc_start: 0.8317 (t-100) cc_final: 0.7739 (t-100)
REVERT: A  227 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7646 (tp30)
REVERT: A  249 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7147 (tmm)
REVERT: A  267 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (mt)
REVERT: A  271 TRP cc_start: 0.5140 (t60) cc_final: 0.4161 (t60)
REVERT: A  307 ILE cc_start: 0.8385 (tp) cc_final: 0.8154 (tt)
REVERT: A  310 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7487 (mm-30)
REVERT: A  313 LYS cc_start: 0.7963 (mttt) cc_final: 0.7643 (ttmm)
REVERT: A  327 PHE cc_start: 0.8965 (t80) cc_final: 0.8722 (t80)
REVERT: A  330 ASN cc_start: 0.8351 (m-40) cc_final: 0.7939 (p0)
REVERT: A  375 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7279 (mm-30)
REVERT: A  406 GLU cc_start: 0.7972 (tp30) cc_final: 0.7764 (tp30)
REVERT: A  429 GLN cc_start: 0.7338 (tp40) cc_final: 0.6978 (tp40)
REVERT: A  465 LYS cc_start: 0.8819 (mttt) cc_final: 0.8360 (ttmt)
REVERT: A  472 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7660 (mm-40)
REVERT: A  475 LYS cc_start: 0.8373 (tppt) cc_final: 0.8101 (tmtt)
REVERT: A  504 PHE cc_start: 0.8105 (t80) cc_final: 0.7600 (t80)
REVERT: A  518 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7607 (tmm-80)
REVERT: A  557 MET cc_start: 0.7904 (tmm) cc_final: 0.7604 (tmm)
REVERT: A  559 ARG cc_start: 0.8237 (ptt180) cc_final: 0.7903 (ptm160)
REVERT: A  564 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7817 (mm-30)
REVERT: A  582 ARG cc_start: 0.7531 (tpp80) cc_final: 0.7098 (tpp80)
REVERT: A  600 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8449 (mmmm)
REVERT: A  603 PHE cc_start: 0.7278 (t80) cc_final: 0.6906 (t80)
  outliers start: 32
  outliers final: 21
  residues processed: 222
  average time/residue: 0.2280
  time to fit residues: 63.5577
Evaluate side-chains
  228 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  387 LEU
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 44 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.4778

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6611  Z= 0.270
  Angle     :  0.680  11.386   8986  Z= 0.334
  Chirality :  0.045   0.134    939
  Planarity :  0.004   0.040   1166
  Dihedral  :  4.736  36.986    861
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 28.02 %
    Favored  : 67.67 %
  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: -1.51 (0.30), residues: 787
  helix: -1.14 (0.26), residues: 366
  sheet: -1.82 (0.69), residues: 48
  loop : -0.54 (0.34), residues: 373

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   0.015   0.002   PHE A 356 
 TYR   0.017   0.001   TYR E 489 
 ARG   0.007   0.001   ARG A 219 

*********************** 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 fitting.
    rotamer outliers: 30
    poor density    : 202
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7838 (mtp85)
REVERT: E  364 ASP cc_start: 0.8196 (t70) cc_final: 0.7953 (t70)
REVERT: E  403 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7729 (ttp80)
REVERT: E  422 ASN cc_start: 0.8203 (m110) cc_final: 0.7817 (m-40)
REVERT: E  442 ASP cc_start: 0.8686 (t70) cc_final: 0.8162 (t0)
REVERT: E  467 ASP cc_start: 0.8319 (p0) cc_final: 0.7739 (p0)
REVERT: E  473 TYR cc_start: 0.7690 (t80) cc_final: 0.7203 (t80)
REVERT: E  494 SER cc_start: 0.8909 (m) cc_final: 0.8461 (p)
REVERT: E  505 HIS cc_start: 0.8371 (m170) cc_final: 0.7956 (m170)
REVERT: A   26 LYS cc_start: 0.8296 (mttt) cc_final: 0.7960 (mmtt)
REVERT: A   31 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7138 (tttt)
REVERT: A   40 PHE cc_start: 0.8561 (t80) cc_final: 0.8297 (t80)
REVERT: A   47 SER cc_start: 0.8725 (t) cc_final: 0.8487 (t)
REVERT: A   55 THR cc_start: 0.7909 (m) cc_final: 0.7313 (p)
REVERT: A   62 MET cc_start: 0.8248 (tmm) cc_final: 0.7354 (tmm)
REVERT: A   75 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: A  121 ASN cc_start: 0.8895 (m-40) cc_final: 0.8571 (m110)
REVERT: A  123 MET cc_start: 0.8480 (ttt) cc_final: 0.8039 (ttp)
REVERT: A  126 ILE cc_start: 0.8920 (tp) cc_final: 0.8663 (tt)
REVERT: A  144 LEU cc_start: 0.8271 (tp) cc_final: 0.7837 (tp)
REVERT: A  157 ASP cc_start: 0.7981 (m-30) cc_final: 0.7604 (t0)
REVERT: A  158 TYR cc_start: 0.6600 (t80) cc_final: 0.6110 (t80)
REVERT: A  160 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7104 (tm-30)
REVERT: A  168 TRP cc_start: 0.8315 (t-100) cc_final: 0.7686 (t-100)
REVERT: A  227 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7636 (tp30)
REVERT: A  249 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7219 (tmm)
REVERT: A  267 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8274 (mm)
REVERT: A  271 TRP cc_start: 0.5060 (t60) cc_final: 0.4090 (t60)
REVERT: A  307 ILE cc_start: 0.8378 (tp) cc_final: 0.8135 (tt)
REVERT: A  310 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7494 (mm-30)
REVERT: A  313 LYS cc_start: 0.7939 (mttt) cc_final: 0.7661 (mtpt)
REVERT: A  327 PHE cc_start: 0.8980 (t80) cc_final: 0.8743 (t80)
REVERT: A  330 ASN cc_start: 0.8428 (m-40) cc_final: 0.7956 (p0)
REVERT: A  375 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7252 (mm-30)
REVERT: A  406 GLU cc_start: 0.8084 (tp30) cc_final: 0.7842 (tp30)
REVERT: A  429 GLN cc_start: 0.7362 (tp40) cc_final: 0.7017 (tp40)
REVERT: A  465 LYS cc_start: 0.8804 (mttt) cc_final: 0.8306 (ttmt)
REVERT: A  475 LYS cc_start: 0.8365 (tppt) cc_final: 0.8103 (tmtt)
REVERT: A  484 ILE cc_start: 0.8890 (mt) cc_final: 0.8630 (mm)
REVERT: A  518 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7624 (tmm-80)
REVERT: A  559 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7897 (ptm160)
REVERT: A  564 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7844 (mt-10)
REVERT: A  582 ARG cc_start: 0.7541 (tpp80) cc_final: 0.7092 (tpp80)
REVERT: A  600 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8438 (mmmm)
REVERT: A  603 PHE cc_start: 0.7291 (t80) cc_final: 0.6914 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 213
  average time/residue: 0.2252
  time to fit residues: 59.8600
Evaluate side-chains
  226 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 59 optimal weight:    0.1980
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 HIS
A 535 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6611  Z= 0.285
  Angle     :  0.694  11.619   8986  Z= 0.343
  Chirality :  0.046   0.145    939
  Planarity :  0.004   0.039   1166
  Dihedral  :  4.747  34.379    861
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.16 %
    Favored  : 67.67 %
  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: -1.32 (0.30), residues: 787
  helix: -0.96 (0.27), residues: 367
  sheet: -1.76 (0.69), residues: 48
  loop : -0.47 (0.34), residues: 372

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   0.016   0.002   PHE A 400 
 TYR   0.017   0.002   TYR A 180 
 ARG   0.007   0.000   ARG A 219 

*********************** 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
  246 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 210
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7827 (mtp85)
REVERT: E  364 ASP cc_start: 0.8246 (t70) cc_final: 0.7982 (t70)
REVERT: E  403 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7810 (ttp80)
REVERT: E  422 ASN cc_start: 0.8230 (m110) cc_final: 0.7827 (m-40)
REVERT: E  442 ASP cc_start: 0.8674 (t70) cc_final: 0.8168 (t0)
REVERT: E  467 ASP cc_start: 0.8331 (p0) cc_final: 0.7712 (p0)
REVERT: E  473 TYR cc_start: 0.7726 (t80) cc_final: 0.7245 (t80)
REVERT: E  494 SER cc_start: 0.8946 (m) cc_final: 0.8587 (p)
REVERT: A   26 LYS cc_start: 0.8277 (mttt) cc_final: 0.7945 (mmtt)
REVERT: A   31 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7060 (tttp)
REVERT: A   40 PHE cc_start: 0.8552 (t80) cc_final: 0.8281 (t80)
REVERT: A   55 THR cc_start: 0.7916 (m) cc_final: 0.7321 (p)
REVERT: A   62 MET cc_start: 0.8285 (tmm) cc_final: 0.7373 (tmm)
REVERT: A   75 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A  110 GLU cc_start: 0.7601 (pm20) cc_final: 0.7212 (pm20)
REVERT: A  123 MET cc_start: 0.8425 (ttt) cc_final: 0.8072 (ttp)
REVERT: A  126 ILE cc_start: 0.8981 (tp) cc_final: 0.8740 (tt)
REVERT: A  144 LEU cc_start: 0.8159 (tp) cc_final: 0.7730 (tp)
REVERT: A  157 ASP cc_start: 0.7968 (m-30) cc_final: 0.7542 (t0)
REVERT: A  158 TYR cc_start: 0.6690 (t80) cc_final: 0.6211 (t80)
REVERT: A  160 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7075 (tm-30)
REVERT: A  166 GLU cc_start: 0.7376 (tp30) cc_final: 0.7036 (tp30)
REVERT: A  168 TRP cc_start: 0.8360 (t-100) cc_final: 0.7686 (t-100)
REVERT: A  227 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7626 (tp30)
REVERT: A  249 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7302 (tmm)
REVERT: A  267 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8283 (mm)
REVERT: A  271 TRP cc_start: 0.5058 (t60) cc_final: 0.4063 (t60)
REVERT: A  307 ILE cc_start: 0.8388 (tp) cc_final: 0.8157 (tt)
REVERT: A  310 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: A  313 LYS cc_start: 0.7943 (mttt) cc_final: 0.7618 (ttmm)
REVERT: A  327 PHE cc_start: 0.8991 (t80) cc_final: 0.8574 (t80)
REVERT: A  330 ASN cc_start: 0.8411 (m-40) cc_final: 0.7909 (p0)
REVERT: A  375 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7250 (mm-30)
REVERT: A  429 GLN cc_start: 0.7346 (tp40) cc_final: 0.6724 (tp40)
REVERT: A  465 LYS cc_start: 0.8770 (mttt) cc_final: 0.8198 (ttmt)
REVERT: A  475 LYS cc_start: 0.8400 (tppt) cc_final: 0.8142 (tmtt)
REVERT: A  559 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (ptm160)
REVERT: A  582 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7128 (tpp80)
REVERT: A  600 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8446 (mmmm)
REVERT: A  603 PHE cc_start: 0.7308 (t80) cc_final: 0.6917 (t80)
REVERT: A  604 VAL cc_start: 0.7990 (m) cc_final: 0.7644 (m)
  outliers start: 36
  outliers final: 21
  residues processed: 221
  average time/residue: 0.2305
  time to fit residues: 64.3683
Evaluate side-chains
  233 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  387 LEU
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  483 VAL
Chi-restraints excluded: chain E residue  500 THR
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  180 TYR
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  608 THR
Chi-restraints excluded: chain A residue  609 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.0060
   chunk 55 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0970
   overall best weight:    0.1772

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
A 505 HIS
A 508 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.5010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6611  Z= 0.186
  Angle     :  0.667  12.243   8986  Z= 0.327
  Chirality :  0.043   0.150    939
  Planarity :  0.004   0.040   1166
  Dihedral  :  4.487  29.343    861
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.17 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.10 (0.31), residues: 787
  helix: -0.74 (0.27), residues: 369
  sheet: -1.70 (0.70), residues: 47
  loop : -0.40 (0.35), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 349 
 HIS   0.004   0.001   HIS E 505 
 PHE   0.015   0.001   PHE A 356 
 TYR   0.013   0.001   TYR A 180 
 ARG   0.006   0.000   ARG A 219 

*********************** 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
  236 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 209
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7783 (mtp85)
REVERT: E  422 ASN cc_start: 0.8139 (m110) cc_final: 0.7749 (m-40)
REVERT: E  442 ASP cc_start: 0.8694 (t70) cc_final: 0.8191 (t0)
REVERT: E  467 ASP cc_start: 0.8262 (p0) cc_final: 0.7767 (p0)
REVERT: E  494 SER cc_start: 0.8740 (m) cc_final: 0.8417 (p)
REVERT: A   26 LYS cc_start: 0.8269 (mttt) cc_final: 0.7966 (mmtt)
REVERT: A   31 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7085 (tttp)
REVERT: A   40 PHE cc_start: 0.8516 (t80) cc_final: 0.8275 (t80)
REVERT: A   55 THR cc_start: 0.7912 (m) cc_final: 0.7342 (p)
REVERT: A   62 MET cc_start: 0.8215 (tmm) cc_final: 0.7351 (tmm)
REVERT: A   82 MET cc_start: 0.7542 (tpp) cc_final: 0.7137 (tpt)
REVERT: A  121 ASN cc_start: 0.8977 (m-40) cc_final: 0.8630 (m110)
REVERT: A  123 MET cc_start: 0.8390 (ttt) cc_final: 0.8167 (ttm)
REVERT: A  126 ILE cc_start: 0.8882 (tp) cc_final: 0.8664 (tt)
REVERT: A  144 LEU cc_start: 0.8037 (tp) cc_final: 0.7836 (tp)
REVERT: A  157 ASP cc_start: 0.7992 (m-30) cc_final: 0.7582 (t0)
REVERT: A  160 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6727 (tm-30)
REVERT: A  168 TRP cc_start: 0.8244 (t-100) cc_final: 0.7540 (t-100)
REVERT: A  227 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7631 (tp30)
REVERT: A  267 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8194 (mm)
REVERT: A  271 TRP cc_start: 0.5060 (t60) cc_final: 0.4162 (t60)
REVERT: A  307 ILE cc_start: 0.8304 (tp) cc_final: 0.8078 (tt)
REVERT: A  310 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: A  313 LYS cc_start: 0.7870 (mttt) cc_final: 0.7550 (mtpt)
REVERT: A  330 ASN cc_start: 0.8265 (m-40) cc_final: 0.7873 (p0)
REVERT: A  332 MET cc_start: 0.7876 (tmm) cc_final: 0.7532 (tmm)
REVERT: A  465 LYS cc_start: 0.8609 (mttt) cc_final: 0.8184 (ttmt)
REVERT: A  475 LYS cc_start: 0.8319 (tppt) cc_final: 0.8076 (tmtt)
REVERT: A  559 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (ptm160)
REVERT: A  564 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7977 (mt-10)
REVERT: A  582 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7067 (tpp80)
REVERT: A  600 LYS cc_start: 0.8662 (mmmm) cc_final: 0.8413 (mmmm)
REVERT: A  603 PHE cc_start: 0.7279 (t80) cc_final: 0.6931 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 221
  average time/residue: 0.2235
  time to fit residues: 62.4455
Evaluate side-chains
  229 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  387 LEU
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  472 ILE
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
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  365 THR
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  468 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.3980
   chunk 71 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0770
   chunk 57 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 ASN
** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6611  Z= 0.286
  Angle     :  0.731  11.809   8986  Z= 0.360
  Chirality :  0.046   0.143    939
  Planarity :  0.004   0.038   1166
  Dihedral  :  4.707  25.930    861
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 30.17 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.04 (0.31), residues: 787
  helix: -0.68 (0.27), residues: 370
  sheet: -1.44 (0.73), residues: 45
  loop : -0.41 (0.35), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 349 
 HIS   0.011   0.001   HIS E 505 
 PHE   0.027   0.002   PHE A 428 
 TYR   0.020   0.002   TYR E 501 
 ARG   0.007   0.000   ARG A 219 

********************** 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
  233 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  357 ARG cc_start: 0.8054 (mtp-110) cc_final: 0.7728 (ttp80)
REVERT: E  403 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7646 (ttp80)
REVERT: E  422 ASN cc_start: 0.8222 (m110) cc_final: 0.7877 (m-40)
REVERT: E  442 ASP cc_start: 0.8675 (t70) cc_final: 0.8146 (t0)
REVERT: E  467 ASP cc_start: 0.8347 (p0) cc_final: 0.7773 (p0)
REVERT: E  473 TYR cc_start: 0.7723 (t80) cc_final: 0.7270 (t80)
REVERT: E  494 SER cc_start: 0.8881 (m) cc_final: 0.8521 (p)
REVERT: A   26 LYS cc_start: 0.8303 (mttt) cc_final: 0.7966 (mmtt)
REVERT: A   31 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7055 (tttp)
REVERT: A   40 PHE cc_start: 0.8572 (t80) cc_final: 0.8315 (t80)
REVERT: A   55 THR cc_start: 0.8065 (m) cc_final: 0.7478 (p)
REVERT: A   62 MET cc_start: 0.8297 (tmm) cc_final: 0.7372 (tmm)
REVERT: A   75 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: A   82 MET cc_start: 0.7621 (tpp) cc_final: 0.7420 (tpt)
REVERT: A  123 MET cc_start: 0.8466 (ttt) cc_final: 0.8084 (ttp)
REVERT: A  126 ILE cc_start: 0.8937 (tp) cc_final: 0.8673 (tt)
REVERT: A  157 ASP cc_start: 0.7958 (m-30) cc_final: 0.7563 (t0)
REVERT: A  160 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6856 (tm-30)
REVERT: A  227 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7638 (tp30)
REVERT: A  267 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8261 (mm)
REVERT: A  271 TRP cc_start: 0.5067 (t60) cc_final: 0.4013 (t60)
REVERT: A  307 ILE cc_start: 0.8371 (tp) cc_final: 0.8127 (tt)
REVERT: A  310 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7437 (mm-30)
REVERT: A  313 LYS cc_start: 0.7836 (mttt) cc_final: 0.7522 (mtpt)
REVERT: A  315 PHE cc_start: 0.8036 (m-80) cc_final: 0.7784 (t80)
REVERT: A  330 ASN cc_start: 0.8409 (m-40) cc_final: 0.7935 (p0)
REVERT: A  332 MET cc_start: 0.7868 (tmm) cc_final: 0.7546 (tmm)
REVERT: A  353 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7699 (mtpp)
REVERT: A  465 LYS cc_start: 0.8659 (mttt) cc_final: 0.8193 (ttmt)
REVERT: A  475 LYS cc_start: 0.8384 (tppt) cc_final: 0.8126 (tmtt)
REVERT: A  559 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7865 (ptm160)
REVERT: A  564 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8008 (mt-10)
REVERT: A  582 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7140 (tpp80)
REVERT: A  600 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8437 (mmmm)
REVERT: A  603 PHE cc_start: 0.7362 (t80) cc_final: 0.6985 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 221
  average time/residue: 0.2234
  time to fit residues: 61.8225
Evaluate side-chains
  223 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  360 ASN
Chi-restraints excluded: chain E residue  387 LEU
Chi-restraints excluded: chain E residue  393 THR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  163 TRP
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  353 LYS
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 63 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 54 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   chunk 70 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
E 360 ASN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.111422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.096320 restraints weight = 12056.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.099785 restraints weight = 5635.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.101971 restraints weight = 3215.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6611  Z= 0.246
  Angle     :  0.721  11.797   8986  Z= 0.351
  Chirality :  0.046   0.148    939
  Planarity :  0.004   0.038   1166
  Dihedral  :  4.745  25.159    861
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 30.03 %
    Favored  : 66.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.94 (0.31), residues: 787
  helix: -0.58 (0.28), residues: 367
  sheet: -1.41 (0.71), residues: 47
  loop : -0.38 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 302 
 HIS   0.010   0.001   HIS E 505 
 PHE   0.014   0.001   PHE A 356 
 TYR   0.021   0.002   TYR E 501 
 ARG   0.007   0.000   ARG A 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2135.86 seconds
wall clock time: 40 minutes 38.28 seconds (2438.28 seconds total)