Starting phenix.real_space_refine
on Sun Aug 24 03:05:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8or2_17115/08_2025/8or2_17115.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8or2_17115/08_2025/8or2_17115.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8or2_17115/08_2025/8or2_17115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8or2_17115/08_2025/8or2_17115.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8or2_17115/08_2025/8or2_17115.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8or2_17115/08_2025/8or2_17115.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     S      99      5.16       5
     C   10554      2.51       5
     N    2816      2.21       5
     O    3086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16558
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 689, 5651
          Classifications: {'peptide': 689}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 677}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 731
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "C"
      Number of atoms: 8808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1132, 8808
          Classifications: {'peptide': 1132}
          Link IDs: {'PTRANS': 53, 'TRANS': 1078}
          Chain breaks: 7
    Chain: "F"
      Number of atoms: 1365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1365
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 7, 'TRANS': 155}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5876  SG  CYS B  45     126.042  64.210  43.049  1.00 56.54           S
  ATOM   6171  SG  CYS B  83     125.084  62.262  46.086  1.00 54.48           S
  ATOM   6100  SG  CYS B  75     126.480  75.706  52.362  1.00 53.89           S
  ATOM   6267  SG  CYS B  94     129.544  72.330  52.823  1.00 53.87           S
  ATOM   5943  SG  CYS B  53     121.363  59.522  43.325  1.00 58.28           S
  ATOM   5966  SG  CYS B  56     118.661  58.356  43.069  1.00 60.30           S
  ATOM   6050  SG  CYS B  68     117.351  61.442  42.096  1.00 55.90           S

  Time building chain proxies: 3.83, per 1000 atoms: 0.23
  Number of scatterers: 16558
  At special positions: 0
  Unit cell: (150.12, 133.92, 166.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      3     29.99
     S      99     16.00
     O    3086      8.00
     N    2816      7.00
     C   10554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 552.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B4001 "
        pdb="ZN    ZN B4001 " - pdb=" ND1 HIS B  80 "
        pdb="ZN    ZN B4001 " - pdb=" SG  CYS B  45 "
        pdb="ZN    ZN B4001 " - pdb=" SG  CYS B  83 "
      pdb="  ZN B4002 "
        pdb="ZN    ZN B4002 " - pdb=" ND1 HIS B  77 "
        pdb="ZN    ZN B4002 " - pdb=" SG  CYS B  94 "
        pdb="ZN    ZN B4002 " - pdb=" SG  CYS B  75 "
      pdb="  ZN B4003 "
        pdb="ZN    ZN B4003 " - pdb=" SG  CYS B  56 "
        pdb="ZN    ZN B4003 " - pdb=" SG  CYS B  68 "
        pdb="ZN    ZN B4003 " - pdb=" SG  CYS B  53 "


  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3998

  Finding SS restraints...
    Secondary structure from input PDB file:
      108 helices and 5 sheets defined
      73.3% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 33
      removed outlier: 3.953A  pdb=" N   GLN A  29 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   TYR A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 54
      removed outlier: 3.531A  pdb=" N   TYR A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 107
    Processing helix  chain 'A' and resid 115 through 137
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 158 through 173
      removed outlier: 3.756A  pdb=" N   ARG A 173 " --> pdb=" O   ASP A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 191
      removed outlier: 3.597A  pdb=" N   GLN A 178 " --> pdb=" O   PRO A 174 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS A 185 " --> pdb=" O   ASN A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 4.032A  pdb=" N   ILE A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.536A  pdb=" N   PHE A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 255
      removed outlier: 3.786A  pdb=" N   GLN A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 279
      removed outlier: 3.600A  pdb=" N   TYR A 260 " --> pdb=" O   PRO A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 296
      removed outlier: 4.378A  pdb=" N   GLU A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS A 290 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 313
      removed outlier: 3.564A  pdb=" N   GLU A 306 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLN A 308 " --> pdb=" O   HIS A 304 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASN A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ALA A 313 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 328
      removed outlier: 3.910A  pdb=" N   ARG A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 355
      removed outlier: 3.643A  pdb=" N   CYS A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 385
    Processing helix  chain 'A' and resid 388 through 405
      removed outlier: 3.900A  pdb=" N   ALA A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA A 394 " --> pdb=" O   GLY A 390 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASN A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN A 405 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 413
    Processing helix  chain 'A' and resid 416 through 431
    Processing helix  chain 'A' and resid 442 through 454
      removed outlier: 3.861A  pdb=" N   LEU A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A 454 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 476
    Processing helix  chain 'A' and resid 481 through 496
      removed outlier: 3.706A  pdb=" N   GLU A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLN A 494 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A 495 " --> pdb=" O   LYS A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 525
    Processing helix  chain 'A' and resid 559 through 572
      removed outlier: 3.604A  pdb=" N   TYR A 563 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE A 566 " --> pdb=" O   SER A 562 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 612
    Processing helix  chain 'A' and resid 621 through 630
    Processing helix  chain 'A' and resid 632 through 646
    Processing helix  chain 'A' and resid 690 through 722
      removed outlier: 3.790A  pdb=" N   MET A 721 " --> pdb=" O   ARG A 717 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A 722 " --> pdb=" O   ILE A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 738
      removed outlier: 3.677A  pdb=" N   LEU A 731 " --> pdb=" O   HIS A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 759
      removed outlier: 3.776A  pdb=" N   LYS A 751 " --> pdb=" O   PRO A 747 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   CYS A 752 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE A 753 " --> pdb=" O   ILE A 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
      removed outlier: 3.852A  pdb=" N   ASN B  41 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 59
      removed outlier: 3.968A  pdb=" N   ASN B  59 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 88
    Processing helix  chain 'C' and resid 5 through 15
    Processing helix  chain 'C' and resid 19 through 23
      removed outlier: 3.518A  pdb=" N   ARG C  23 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 36
    Processing helix  chain 'C' and resid 42 through 57
    Processing helix  chain 'C' and resid 61 through 78
      removed outlier: 3.893A  pdb=" N   GLY C  73 " --> pdb=" O   VAL C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
      removed outlier: 3.742A  pdb=" N   SER C  77 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS C  78 " --> pdb=" O   PRO C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 96
      removed outlier: 3.674A  pdb=" N   VAL C  84 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 117
    Processing helix  chain 'C' and resid 128 through 142
    Processing helix  chain 'C' and resid 148 through 165
    Processing helix  chain 'C' and resid 169 through 171
      No H-bonds generated for 'chain 'C' and resid 169 through 171'
    Processing helix  chain 'C' and resid 172 through 181
    Processing helix  chain 'C' and resid 182 through 186
    Processing helix  chain 'C' and resid 188 through 206
      removed outlier: 3.860A  pdb=" N   MET C 204 " --> pdb=" O   GLY C 200 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   SER C 205 " --> pdb=" O   HIS C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 226
      removed outlier: 4.431A  pdb=" N   GLU C 216 " --> pdb=" O   VAL C 212 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   HIS C 217 " --> pdb=" O   ASP C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 245
    Processing helix  chain 'C' and resid 249 through 253
      removed outlier: 4.050A  pdb=" N   LEU C 253 " --> pdb=" O   GLY C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 264
    Processing helix  chain 'C' and resid 270 through 285
      removed outlier: 4.333A  pdb=" N   TYR C 274 " --> pdb=" O   GLU C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 304
      removed outlier: 3.556A  pdb=" N   VAL C 294 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR C 296 " --> pdb=" O   PRO C 292 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ILE C 297 " --> pdb=" O   HIS C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 363
      removed outlier: 3.806A  pdb=" N   ARG C 350 " --> pdb=" O   SER C 346 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU C 357 " --> pdb=" O   ALA C 353 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP C 358 " --> pdb=" O   ALA C 354 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ALA C 359 " --> pdb=" O   LYS C 355 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   VAL C 360 " --> pdb=" O   CYS C 356 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 374
    Processing helix  chain 'C' and resid 375 through 383
    Processing helix  chain 'C' and resid 387 through 406
      removed outlier: 3.633A  pdb=" N   ASP C 393 " --> pdb=" O   ASN C 389 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG C 406 " --> pdb=" O   LEU C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 443
      removed outlier: 3.639A  pdb=" N   GLN C 431 " --> pdb=" O   MET C 427 " (cutoff:3.500A)
      Proline residue:  C 433  - end of helix
      removed outlier: 3.870A  pdb=" N   LYS C 437 " --> pdb=" O   PRO C 433 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA C 438 " --> pdb=" O   ASN C 434 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS C 441 " --> pdb=" O   LYS C 437 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLN C 442 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 447 through 465
    Processing helix  chain 'C' and resid 472 through 486
      Proline residue:  C 478  - end of helix
    Processing helix  chain 'C' and resid 490 through 507
    Processing helix  chain 'C' and resid 508 through 515
      removed outlier: 6.121A  pdb=" N   GLN C 511 " --> pdb=" O   HIS C 508 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   HIS C 514 " --> pdb=" O   GLN C 511 " (cutoff:3.500A)
      Proline residue:  C 515  - end of helix
    Processing helix  chain 'C' and resid 516 through 529
      Proline residue:  C 522  - end of helix
      removed outlier: 3.548A  pdb=" N   GLY C 529 " --> pdb=" O   VAL C 525 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 532 through 551
      removed outlier: 3.518A  pdb=" N   LYS C 548 " --> pdb=" O   GLN C 544 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG C 551 " --> pdb=" O   VAL C 547 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 561 through 563
      No H-bonds generated for 'chain 'C' and resid 561 through 563'
    Processing helix  chain 'C' and resid 564 through 577
      removed outlier: 4.197A  pdb=" N   ARG C 575 " --> pdb=" O   CYS C 571 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS C 577 " --> pdb=" O   ILE C 573 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 582 through 600
    Processing helix  chain 'C' and resid 606 through 621
      removed outlier: 4.700A  pdb=" N   ASN C 610 " --> pdb=" O   SER C 606 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   THR C 611 " --> pdb=" O   ASP C 607 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE C 614 " --> pdb=" O   ASN C 610 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   PHE C 615 " --> pdb=" O   THR C 611 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU C 616 " --> pdb=" O   LEU C 612 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLU C 617 " --> pdb=" O   GLN C 613 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS C 620 " --> pdb=" O   LEU C 616 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ASN C 621 " --> pdb=" O   GLU C 617 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 624 through 637
    Processing helix  chain 'C' and resid 644 through 648
    Processing helix  chain 'C' and resid 651 through 657
    Processing helix  chain 'C' and resid 658 through 660
      No H-bonds generated for 'chain 'C' and resid 658 through 660'
    Processing helix  chain 'C' and resid 663 through 681
    Processing helix  chain 'C' and resid 686 through 695
    Processing helix  chain 'C' and resid 706 through 723
    Processing helix  chain 'C' and resid 733 through 743
      removed outlier: 3.768A  pdb=" N   ARG C 743 " --> pdb=" O   ILE C 739 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 749 through 766
      removed outlier: 3.829A  pdb=" N   SER C 753 " --> pdb=" O   GLY C 749 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 771 through 780
    Processing helix  chain 'C' and resid 792 through 810
    Processing helix  chain 'C' and resid 813 through 826
      removed outlier: 3.858A  pdb=" N   VAL C 817 " --> pdb=" O   GLU C 813 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL C 818 " --> pdb=" O   GLY C 814 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 831 through 846
    Processing helix  chain 'C' and resid 856 through 866
      removed outlier: 3.588A  pdb=" N   VAL C 860 " --> pdb=" O   GLU C 856 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER C 866 " --> pdb=" O   LEU C 862 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 870 through 887
      removed outlier: 3.603A  pdb=" N   VAL C 885 " --> pdb=" O   GLY C 881 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLY C 886 " --> pdb=" O   SER C 882 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASN C 887 " --> pdb=" O   ILE C 883 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 887 through 902
      Proline residue:  C 893  - end of helix
      removed outlier: 3.725A  pdb=" N   THR C 900 " --> pdb=" O   LEU C 896 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 905 through 920
      removed outlier: 3.873A  pdb=" N   HIS C 911 " --> pdb=" O   TYR C 907 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU C 915 " --> pdb=" O   HIS C 911 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE C 916 " --> pdb=" O   SER C 912 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER C 918 " --> pdb=" O   LYS C 914 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 921 through 926
    Processing helix  chain 'C' and resid 929 through 941
      removed outlier: 4.365A  pdb=" N   GLU C 941 " --> pdb=" O   LEU C 937 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 944 through 959
    Processing helix  chain 'C' and resid 962 through 977
      Proline residue:  C 968  - end of helix
      removed outlier: 3.511A  pdb=" N   LEU C 974 " --> pdb=" O   LEU C 970 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE C 975 " --> pdb=" O   LYS C 971 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   SER C 976 " --> pdb=" O   GLY C 972 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 978 through 991
      removed outlier: 3.871A  pdb=" N   PHE C 991 " --> pdb=" O   THR C 987 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1000 through 1014
      removed outlier: 4.248A  pdb=" N   GLY C1009 " --> pdb=" O   LYS C1005 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   ASP C1010 " --> pdb=" O   ASN C1006 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE C1011 " --> pdb=" O   CYS C1007 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1019 through 1037
    Processing helix  chain 'C' and resid 1044 through 1057
      Proline residue:  C1050  - end of helix
      removed outlier: 3.938A  pdb=" N   LYS C1057 " --> pdb=" O   TYR C1053 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1078 through 1092
      removed outlier: 3.662A  pdb=" N   ARG C1082 " --> pdb=" O   GLY C1078 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1102 through 1113
      removed outlier: 3.620A  pdb=" N   ASN C1107 " --> pdb=" O   PHE C1103 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   HIS C1108 " --> pdb=" O   GLU C1104 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL C1109 " --> pdb=" O   PHE C1105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1116 through 1131
    Processing helix  chain 'C' and resid 1134 through 1140
      removed outlier: 3.600A  pdb=" N   VAL C1138 " --> pdb=" O   CYS C1134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1141 through 1154
      Proline residue:  C1148  - end of helix
    Processing helix  chain 'C' and resid 1162 through 1185
      removed outlier: 3.596A  pdb=" N   PHE C1166 " --> pdb=" O   VAL C1162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1201 through 1204
    Processing helix  chain 'C' and resid 1205 through 1210
    Processing helix  chain 'F' and resid 65 through 73
    Processing helix  chain 'F' and resid 99 through 109
      removed outlier: 4.161A  pdb=" N   LEU F 103 " --> pdb=" O   SER F  99 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS F 108 " --> pdb=" O   ILE F 104 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE F 109 " --> pdb=" O   ILE F 105 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 134 through 150
      Proline residue:  F 142  - end of helix
      removed outlier: 3.859A  pdb=" N   GLU F 150 " --> pdb=" O   GLN F 146 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 152 through 166
      removed outlier: 3.822A  pdb=" N   ASP F 156 " --> pdb=" O   GLY F 152 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE F 162 " --> pdb=" O   TYR F 158 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASN F 163 " --> pdb=" O   GLN F 159 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 174 through 186
      removed outlier: 3.548A  pdb=" N   ALA F 178 " --> pdb=" O   ASP F 174 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 192 through 199
    Processing helix  chain 'F' and resid 209 through 223
      removed outlier: 3.709A  pdb=" N   TRP F 213 " --> pdb=" O   PRO F 209 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   LEU F 217 " --> pdb=" O   TRP F 213 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   ASP F 218 " --> pdb=" O   ASN F 214 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 239 through 251
      Proline residue:  F 249  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 541
      removed outlier: 6.686A  pdb=" N   SER A 536 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   ALA B  31 " --> pdb=" O   SER A 536 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   GLN A 538 " --> pdb=" O   ALA B  31 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   TRP B  33 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU A 540 " --> pdb=" O   TRP B  33 " (cutoff:3.500A)
      removed outlier: 9.160A  pdb=" N   TRP B  35 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 9.727A  pdb=" N   VAL B  24 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
      removed outlier: 10.748A  pdb=" N   GLY A 588 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 12.651A  pdb=" N   LYS B  26 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
      removed outlier: 11.561A  pdb=" N   SER A 586 " --> pdb=" O   LYS B  26 " (cutoff:3.500A)
      removed outlier: 11.359A  pdb=" N   ASN B  28 " --> pdb=" O   GLN A 584 " (cutoff:3.500A)
      removed outlier: 8.676A  pdb=" N   GLN A 584 " --> pdb=" O   ASN B  28 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL B  30 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR A 600 " --> pdb=" O   VAL A 682 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 726
    Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 71
    Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 94
      removed outlier: 3.691A  pdb=" N   ARG B  99 " --> pdb=" O   CYS B  94 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1063 through 1066
      removed outlier: 3.727A  pdb=" N   VAL C1066 " --> pdb=" O   HIS C1073 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   HIS C1073 " --> pdb=" O   VAL C1066 " (cutoff:3.500A)

    965 hydrogen bonds defined for protein.
    2862 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.51

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 2763
        1.28 -     1.41: 3876
        1.41 -     1.54: 10033
        1.54 -     1.68: 15
        1.68 -     1.81: 148
  Bond restraints: 16835
  Sorted by residual:
  bond pdb=" C   VAL A 724 "
       pdb=" O   VAL A 724 "
    ideal  model  delta    sigma   weight residual
    1.236  1.145  0.091 1.19e-02 7.06e+03 5.91e+01
  bond pdb=" CA  ILE A 755 "
       pdb=" C   ILE A 755 "
    ideal  model  delta    sigma   weight residual
    1.524  1.425  0.099 1.30e-02 5.92e+03 5.77e+01
  bond pdb=" C   ARG B  91 "
       pdb=" N   GLN B  92 "
    ideal  model  delta    sigma   weight residual
    1.333  1.450 -0.117 1.55e-02 4.16e+03 5.69e+01
  bond pdb=" C   LYS A 720 "
       pdb=" O   LYS A 720 "
    ideal  model  delta    sigma   weight residual
    1.237  1.153  0.084 1.19e-02 7.06e+03 4.98e+01
  bond pdb=" C   PRO F 209 "
       pdb=" O   PRO F 209 "
    ideal  model  delta    sigma   weight residual
    1.233  1.151  0.082 1.18e-02 7.18e+03 4.87e+01
  ... (remaining 16830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 22351
        2.58 -     5.17: 305
        5.17 -     7.75: 49
        7.75 -    10.33: 16
       10.33 -    12.92: 10
  Bond angle restraints: 22731
  Sorted by residual:
  angle pdb=" N   ALA F 235 "
        pdb=" CA  ALA F 235 "
        pdb=" C   ALA F 235 "
      ideal   model   delta    sigma   weight residual
     113.01  125.11  -12.10 1.20e+00 6.94e-01 1.02e+02
  angle pdb=" N   VAL A 658 "
        pdb=" CA  VAL A 658 "
        pdb=" C   VAL A 658 "
      ideal   model   delta    sigma   weight residual
     110.72  120.81  -10.09 1.01e+00 9.80e-01 9.99e+01
  angle pdb=" N   VAL F 238 "
        pdb=" CA  VAL F 238 "
        pdb=" C   VAL F 238 "
      ideal   model   delta    sigma   weight residual
     112.98  125.45  -12.47 1.25e+00 6.40e-01 9.95e+01
  angle pdb=" N   SER C  17 "
        pdb=" CA  SER C  17 "
        pdb=" C   SER C  17 "
      ideal   model   delta    sigma   weight residual
     112.54  124.11  -11.57 1.22e+00 6.72e-01 8.99e+01
  angle pdb=" O   GLN B  92 "
        pdb=" C   GLN B  92 "
        pdb=" N   VAL B  93 "
      ideal   model   delta    sigma   weight residual
     122.46  109.60   12.86 1.37e+00 5.33e-01 8.82e+01
  ... (remaining 22726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 9213
       17.99 -    35.98: 952
       35.98 -    53.97: 158
       53.97 -    71.96: 26
       71.96 -    89.95: 14
  Dihedral angle restraints: 10363
    sinusoidal: 4245
      harmonic: 6118
  Sorted by residual:
  dihedral pdb=" N   TYR A 772 "
           pdb=" C   TYR A 772 "
           pdb=" CA  TYR A 772 "
           pdb=" CB  TYR A 772 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.11   15.69     0      2.50e+00 1.60e-01 3.94e+01
  dihedral pdb=" C   VAL F 238 "
           pdb=" N   VAL F 238 "
           pdb=" CA  VAL F 238 "
           pdb=" CB  VAL F 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.16   15.16     0      2.50e+00 1.60e-01 3.68e+01
  dihedral pdb=" N   VAL F 238 "
           pdb=" C   VAL F 238 "
           pdb=" CA  VAL F 238 "
           pdb=" CB  VAL F 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  138.07  -14.67     0      2.50e+00 1.60e-01 3.45e+01
  ... (remaining 10360 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 2583
       0.139 -    0.278: 34
       0.278 -    0.418: 13
       0.418 -    0.557: 5
       0.557 -    0.696: 6
  Chirality restraints: 2641
  Sorted by residual:
  chirality pdb=" CA  ALA F 235 "
            pdb=" N   ALA F 235 "
            pdb=" C   ALA F 235 "
            pdb=" CB  ALA F 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.79    0.70 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CA  VAL F 238 "
            pdb=" N   VAL F 238 "
            pdb=" C   VAL F 238 "
            pdb=" CB  VAL F 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.77    0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" CA  THR F 212 "
            pdb=" N   THR F 212 "
            pdb=" C   THR F 212 "
            pdb=" CB  THR F 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.89    0.64 2.00e-01 2.50e+01 1.01e+01
  ... (remaining 2638 not shown)

  Planarity restraints: 2869
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 772 "    0.075 2.00e-02 2.50e+03   3.81e-02 2.91e+01
        pdb=" CG  TYR A 772 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 772 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 772 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 772 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 772 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 772 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A 772 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 681 "   -0.024 2.00e-02 2.50e+03   4.86e-02 2.36e+01
        pdb=" C   ARG A 681 "    0.084 2.00e-02 2.50e+03
        pdb=" O   ARG A 681 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   VAL A 682 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C1060 "   -0.024 2.00e-02 2.50e+03   4.78e-02 2.28e+01
        pdb=" C   LYS C1060 "    0.083 2.00e-02 2.50e+03
        pdb=" O   LYS C1060 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   GLU C1061 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 2866 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 52
        2.42 -     3.04: 11075
        3.04 -     3.66: 24143
        3.66 -     4.28: 33845
        4.28 -     4.90: 57547
  Nonbonded interactions: 126662
  Sorted by model distance:
  nonbonded pdb=" CB  HIS A 727 "
            pdb=" OD1 ASP A 770 "
     model   vdw
     1.805 3.440
  nonbonded pdb=" O   ILE C 654 "
            pdb=" OG  SER C 657 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   PRO C 893 "
            pdb=" NE2 GLN C 897 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" O   GLN A 463 "
            pdb=" OH  TYR A 500 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   THR C 624 "
            pdb=" OG1 THR C 628 "
     model   vdw
     2.139 3.040
  ... (remaining 126657 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.100
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
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      :  0.007   0.127  16844  Z= 0.461
  Angle     :  0.761  12.916  22731  Z= 0.486
  Chirality :  0.058   0.696   2641
  Planarity :  0.004   0.049   2869
  Dihedral  : 14.647  89.947   6365
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.30 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  1.50 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.65 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.21), residues: 2032
  helix:  2.50 (0.15), residues: 1388
  sheet: -1.91 (1.31), residues: 12
  loop : -1.45 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 764 
 TYR   0.075   0.002   TYR A 772 
 PHE   0.029   0.001   PHE C  24 
 TRP   0.031   0.001   TRP F 213 
 HIS   0.004   0.000   HIS C 847 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 (16835)
  covalent geometry    : angle       0.76102 (22731)
  hydrogen bonds       : bond        0.16105 (  965)
  hydrogen bonds       : angle       5.38273 ( 2862)
  metal coordination   : bond        0.00359 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 341
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 GLU cc_start: 0.7052 (tp30) cc_final: 0.6822 (tp30)
REVERT: A  518 ASN cc_start: 0.7411 (t0) cc_final: 0.7191 (t0)
REVERT: A  655 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5359 (t0)
REVERT: A  657 ASN cc_start: 0.6500 (OUTLIER) cc_final: 0.5299 (t0)
REVERT: A  659 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5670 (m-30)
REVERT: A  676 LYS cc_start: 0.6028 (mmmt) cc_final: 0.5682 (mmtt)
REVERT: C   20 LYS cc_start: 0.7553 (tmtm) cc_final: 0.7315 (ttmt)
REVERT: C   21 ASP cc_start: 0.6796 (m-30) cc_final: 0.6493 (m-30)
REVERT: C  348 LYS cc_start: 0.6996 (ptpp) cc_final: 0.6734 (ptpp)
REVERT: C  441 LYS cc_start: 0.7947 (mptt) cc_final: 0.7687 (mptt)
REVERT: C  457 MET cc_start: 0.7055 (tpp) cc_final: 0.6606 (tpp)
REVERT: C  834 ILE cc_start: 0.6783 (mp) cc_final: 0.6559 (mp)
REVERT: C  890 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6896 (tm-30)
REVERT: C 1106 LEU cc_start: 0.7687 (mp) cc_final: 0.6607 (tt)
  outliers start: 23
  outliers final: 13
  residues processed: 359
  average time/residue: 0.1244
  time to fit residues: 66.9924
Evaluate side-chains
  334 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 318
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  655 ASN
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  659 ASP
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  665 PRO
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain F residue  173 LEU
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain F residue  221 THR
Chi-restraints excluded: chain F residue  231 ASP
Chi-restraints excluded: chain F residue  238 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 194 optimal weight:    0.0470
   chunk 107 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.0020
   chunk 103 optimal weight:    0.6980
   chunk 200 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.1824

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C 151 GLN
** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 847 HIS
C 848 HIS
F 159 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.169018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.152917 restraints weight = 25245.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 1.93
r_work: 0.3978 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3842 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16844  Z= 0.127
  Angle     :  0.563  10.858  22731  Z= 0.285
  Chirality :  0.038   0.154   2641
  Planarity :  0.004   0.058   2869
  Dihedral  :  4.414  58.972   2247
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.11 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.20), residues: 2032
  helix:  2.19 (0.15), residues: 1421
  sheet: -1.72 (1.25), residues: 12
  loop : -1.59 (0.24), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 743 
 TYR   0.024   0.001   TYR A 377 
 PHE   0.025   0.001   PHE F 162 
 TRP   0.019   0.001   TRP F 236 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (16835)
  covalent geometry    : angle       0.56349 (22731)
  hydrogen bonds       : bond        0.03841 (  965)
  hydrogen bonds       : angle       3.80689 ( 2862)
  metal coordination   : bond        0.00574 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 336
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.5124 (mmt) cc_final: 0.4782 (mmt)
REVERT: A  102 ASN cc_start: 0.7484 (t0) cc_final: 0.7254 (t0)
REVERT: A  263 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6743 (mmtt)
REVERT: A  518 ASN cc_start: 0.7696 (t0) cc_final: 0.7446 (t0)
REVERT: A  643 LEU cc_start: 0.7906 (mm) cc_final: 0.7652 (mp)
REVERT: A  647 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8179 (tppt)
REVERT: A  676 LYS cc_start: 0.6504 (mmmt) cc_final: 0.6202 (mmtt)
REVERT: A  702 ASN cc_start: 0.7821 (m110) cc_final: 0.7457 (m110)
REVERT: A  775 LEU cc_start: 0.8707 (pt) cc_final: 0.8460 (pp)
REVERT: C   15 MET cc_start: 0.7739 (mtp) cc_final: 0.7465 (mtp)
REVERT: C   21 ASP cc_start: 0.7311 (m-30) cc_final: 0.7033 (m-30)
REVERT: C  443 MET cc_start: 0.6794 (mmt) cc_final: 0.5767 (mmt)
REVERT: C  691 ASP cc_start: 0.7931 (t0) cc_final: 0.7133 (t0)
REVERT: C  695 ASP cc_start: 0.7377 (m-30) cc_final: 0.6925 (m-30)
REVERT: C  743 ARG cc_start: 0.7141 (ptp90) cc_final: 0.6921 (ptp90)
REVERT: C  834 ILE cc_start: 0.6980 (mp) cc_final: 0.6704 (mp)
REVERT: C  844 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: C  871 GLU cc_start: 0.7134 (pm20) cc_final: 0.6859 (pm20)
REVERT: C  890 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: C 1052 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7790 (tt)
REVERT: C 1090 TYR cc_start: 0.7102 (t80) cc_final: 0.6445 (t80)
REVERT: C 1106 LEU cc_start: 0.7591 (mp) cc_final: 0.6543 (tt)
REVERT: C 1121 MET cc_start: 0.5963 (mtp) cc_final: 0.5699 (mtp)
REVERT: C 1142 LEU cc_start: 0.7684 (tt) cc_final: 0.7408 (tp)
REVERT: F  208 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7481 (pp)
REVERT: F  238 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7292 (t)
  outliers start: 23
  outliers final: 11
  residues processed: 349
  average time/residue: 0.1209
  time to fit residues: 62.9421
Evaluate side-chains
  330 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 316
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue  735 LEU
Chi-restraints excluded: chain C residue  755 MET
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  238 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 142 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9980
   chunk 133 optimal weight:    0.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN
** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 847 HIS
C1108 HIS
F 114 GLN
F 214 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.153245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.136609 restraints weight = 24688.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 1.88
r_work: 0.3749 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  16844  Z= 0.187
  Angle     :  0.632   8.591  22731  Z= 0.323
  Chirality :  0.042   0.159   2641
  Planarity :  0.004   0.046   2869
  Dihedral  :  3.869  50.634   2225
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.06 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.19), residues: 2032
  helix:  1.65 (0.14), residues: 1420
  sheet: -1.70 (1.09), residues: 12
  loop : -1.67 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 588 
 TYR   0.037   0.002   TYR C1117 
 PHE   0.039   0.002   PHE A 569 
 TRP   0.013   0.002   TRP A 581 
 HIS   0.007   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (16835)
  covalent geometry    : angle       0.63226 (22731)
  hydrogen bonds       : bond        0.05428 (  965)
  hydrogen bonds       : angle       3.83038 ( 2862)
  metal coordination   : bond        0.00923 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 358
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.6077 (mmp) cc_final: 0.5495 (mmt)
REVERT: A  143 HIS cc_start: 0.5709 (OUTLIER) cc_final: 0.5420 (m90)
REVERT: A  162 LEU cc_start: 0.8374 (tt) cc_final: 0.8172 (mt)
REVERT: A  204 VAL cc_start: 0.7981 (t) cc_final: 0.7655 (m)
REVERT: A  209 VAL cc_start: 0.8333 (p) cc_final: 0.7937 (t)
REVERT: A  250 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7343 (mm-30)
REVERT: A  261 MET cc_start: 0.7587 (mtp) cc_final: 0.7320 (mtm)
REVERT: A  292 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7504 (mt-10)
REVERT: A  377 TYR cc_start: 0.7454 (m-10) cc_final: 0.7215 (m-80)
REVERT: A  643 LEU cc_start: 0.7983 (mm) cc_final: 0.7712 (mp)
REVERT: A  662 GLU cc_start: 0.7420 (pp20) cc_final: 0.7196 (pp20)
REVERT: B   47 ASN cc_start: 0.8370 (m110) cc_final: 0.8100 (m-40)
REVERT: C   21 ASP cc_start: 0.7327 (m-30) cc_final: 0.7097 (m-30)
REVERT: C   85 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7617 (mm-30)
REVERT: C  156 ASP cc_start: 0.7815 (m-30) cc_final: 0.7553 (m-30)
REVERT: C  549 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7709 (p)
REVERT: C  691 ASP cc_start: 0.7932 (t0) cc_final: 0.7185 (t0)
REVERT: C  695 ASP cc_start: 0.7550 (m-30) cc_final: 0.6963 (m-30)
REVERT: C  860 VAL cc_start: 0.7765 (p) cc_final: 0.7513 (m)
REVERT: C  871 GLU cc_start: 0.7576 (pm20) cc_final: 0.7211 (pm20)
REVERT: C  874 SER cc_start: 0.8258 (t) cc_final: 0.8032 (p)
REVERT: C  890 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7956 (tp30)
REVERT: C 1106 LEU cc_start: 0.7924 (mp) cc_final: 0.6942 (tt)
REVERT: C 1121 MET cc_start: 0.6710 (mtp) cc_final: 0.6274 (mmm)
REVERT: C 1142 LEU cc_start: 0.7865 (tt) cc_final: 0.7633 (tp)
REVERT: C 1168 LYS cc_start: 0.7401 (mmmt) cc_final: 0.7118 (mtpp)
REVERT: F  162 PHE cc_start: 0.6231 (t80) cc_final: 0.5693 (t80)
REVERT: F  208 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7562 (pp)
REVERT: F  238 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7087 (t)
  outliers start: 40
  outliers final: 24
  residues processed: 377
  average time/residue: 0.1454
  time to fit residues: 81.0371
Evaluate side-chains
  359 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 331
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  430 SER
Chi-restraints excluded: chain C residue  469 LEU
Chi-restraints excluded: chain C residue  549 VAL
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  755 MET
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1113 LEU
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Chi-restraints excluded: chain F residue  238 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 179 optimal weight:    0.7980
   chunk 193 optimal weight:    2.9990
   chunk 117 optimal weight:    0.3980
   chunk 116 optimal weight:    0.9980
   chunk 161 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 59 optimal weight:    0.1980
   chunk 121 optimal weight:    0.0870
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 518 ASN
A 520 GLN
A 737 GLN
C 603 ASN
C 847 HIS
F 214 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.152596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.135805 restraints weight = 24334.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 1.92
r_work: 0.3749 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16844  Z= 0.128
  Angle     :  0.564  12.147  22731  Z= 0.283
  Chirality :  0.038   0.158   2641
  Planarity :  0.004   0.046   2869
  Dihedral  :  3.746  51.459   2225
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.80 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.19), residues: 2032
  helix:  1.76 (0.14), residues: 1423
  sheet: -1.61 (1.16), residues: 12
  loop : -1.68 (0.23), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 741 
 TYR   0.024   0.001   TYR C1117 
 PHE   0.016   0.001   PHE C 383 
 TRP   0.007   0.001   TRP F 182 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (16835)
  covalent geometry    : angle       0.56377 (22731)
  hydrogen bonds       : bond        0.04403 (  965)
  hydrogen bonds       : angle       3.65593 ( 2862)
  metal coordination   : bond        0.00440 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 330
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.6143 (mmp) cc_final: 0.5510 (mmt)
REVERT: A  143 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5414 (m90)
REVERT: A  204 VAL cc_start: 0.7924 (t) cc_final: 0.7526 (m)
REVERT: A  209 VAL cc_start: 0.8390 (p) cc_final: 0.8038 (t)
REVERT: A  250 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7306 (mm-30)
REVERT: A  377 TYR cc_start: 0.7566 (m-10) cc_final: 0.7326 (m-80)
REVERT: A  643 LEU cc_start: 0.8004 (mm) cc_final: 0.7762 (mp)
REVERT: A  742 PHE cc_start: 0.7739 (p90) cc_final: 0.7498 (p90)
REVERT: A  743 LYS cc_start: 0.7761 (mptt) cc_final: 0.7435 (mptt)
REVERT: B   47 ASN cc_start: 0.8298 (m110) cc_final: 0.8038 (m-40)
REVERT: B   50 MET cc_start: 0.6923 (mmm) cc_final: 0.6709 (mmm)
REVERT: C   52 MET cc_start: 0.8571 (tpp) cc_final: 0.8342 (tpp)
REVERT: C  156 ASP cc_start: 0.7811 (m-30) cc_final: 0.7541 (m-30)
REVERT: C  457 MET cc_start: 0.7593 (tpp) cc_final: 0.7209 (tpp)
REVERT: C  481 ILE cc_start: 0.7907 (mm) cc_final: 0.7681 (mt)
REVERT: C  691 ASP cc_start: 0.7883 (t0) cc_final: 0.7202 (t0)
REVERT: C  695 ASP cc_start: 0.7527 (m-30) cc_final: 0.6962 (m-30)
REVERT: C  826 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7243 (mtmm)
REVERT: C  860 VAL cc_start: 0.7772 (p) cc_final: 0.7533 (m)
REVERT: C  871 GLU cc_start: 0.7621 (pm20) cc_final: 0.7411 (mp0)
REVERT: C  890 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7956 (tp30)
REVERT: C  897 GLN cc_start: 0.7803 (mp10) cc_final: 0.7391 (tm-30)
REVERT: C 1106 LEU cc_start: 0.7887 (mp) cc_final: 0.6981 (tt)
REVERT: C 1121 MET cc_start: 0.6543 (mtp) cc_final: 0.6182 (mmm)
REVERT: C 1142 LEU cc_start: 0.7883 (tt) cc_final: 0.7648 (tp)
REVERT: C 1168 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7118 (mtpp)
REVERT: F  208 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7568 (pp)
  outliers start: 45
  outliers final: 27
  residues processed: 354
  average time/residue: 0.1470
  time to fit residues: 76.3425
Evaluate side-chains
  344 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 315
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  430 SER
Chi-restraints excluded: chain C residue  610 ASN
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1113 LEU
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 185 optimal weight:    0.9990
   chunk 168 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 151 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 518 ASN
A 655 ASN
B  59 ASN
C 662 ASN
C1164 GLN
F 197 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.147898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.131125 restraints weight = 24217.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 1.90
r_work: 0.3671 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16844  Z= 0.170
  Angle     :  0.624  13.100  22731  Z= 0.315
  Chirality :  0.041   0.168   2641
  Planarity :  0.004   0.048   2869
  Dihedral  :  3.959  43.187   2224
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.82 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.19), residues: 2032
  helix:  1.51 (0.14), residues: 1426
  sheet: -0.15 (1.07), residues: 24
  loop : -1.79 (0.23), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 588 
 TYR   0.029   0.002   TYR C1117 
 PHE   0.026   0.002   PHE A 566 
 TRP   0.021   0.002   TRP A 167 
 HIS   0.008   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (16835)
  covalent geometry    : angle       0.62385 (22731)
  hydrogen bonds       : bond        0.05419 (  965)
  hydrogen bonds       : angle       3.83178 ( 2862)
  metal coordination   : bond        0.00790 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 331
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.6677 (mmp) cc_final: 0.5907 (mmt)
REVERT: A  109 ASP cc_start: 0.6206 (p0) cc_final: 0.5989 (p0)
REVERT: A  143 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.5398 (m90)
REVERT: A  204 VAL cc_start: 0.7960 (t) cc_final: 0.7604 (m)
REVERT: A  209 VAL cc_start: 0.8579 (p) cc_final: 0.8301 (t)
REVERT: A  353 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8087 (tt0)
REVERT: A  643 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7885 (mp)
REVERT: A  743 LYS cc_start: 0.7829 (mptt) cc_final: 0.7607 (mptt)
REVERT: B   50 MET cc_start: 0.7102 (mmm) cc_final: 0.6859 (mmm)
REVERT: C   46 GLU cc_start: 0.7123 (tp30) cc_final: 0.6877 (tp30)
REVERT: C  156 ASP cc_start: 0.7867 (m-30) cc_final: 0.7551 (m-30)
REVERT: C  279 PHE cc_start: 0.6684 (t80) cc_final: 0.6427 (t80)
REVERT: C  662 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7809 (p0)
REVERT: C  691 ASP cc_start: 0.7915 (t0) cc_final: 0.7176 (t0)
REVERT: C  695 ASP cc_start: 0.7635 (m-30) cc_final: 0.6898 (m-30)
REVERT: C  696 GLU cc_start: 0.6546 (mp0) cc_final: 0.6266 (mp0)
REVERT: C  748 GLN cc_start: 0.7908 (pp30) cc_final: 0.7631 (pp30)
REVERT: C  821 PHE cc_start: 0.6843 (m-10) cc_final: 0.6408 (m-10)
REVERT: C  890 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8038 (tp30)
REVERT: C  897 GLN cc_start: 0.7821 (mp10) cc_final: 0.7427 (tm-30)
REVERT: C  915 GLU cc_start: 0.8455 (mp0) cc_final: 0.8115 (mp0)
REVERT: C  969 ARG cc_start: 0.7588 (mtp180) cc_final: 0.7354 (mtp180)
REVERT: C 1017 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.5348 (m-30)
REVERT: C 1073 HIS cc_start: 0.7145 (t-90) cc_final: 0.6697 (t-170)
REVERT: C 1106 LEU cc_start: 0.7843 (mp) cc_final: 0.6978 (tt)
REVERT: C 1121 MET cc_start: 0.6785 (mtp) cc_final: 0.6421 (mmm)
REVERT: C 1142 LEU cc_start: 0.7906 (tt) cc_final: 0.7702 (tp)
REVERT: C 1168 LYS cc_start: 0.7398 (mmmt) cc_final: 0.7081 (mtpp)
REVERT: F  208 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7702 (pp)
  outliers start: 61
  outliers final: 40
  residues processed: 369
  average time/residue: 0.1267
  time to fit residues: 68.7811
Evaluate side-chains
  364 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 319
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  430 SER
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  662 ASN
Chi-restraints excluded: chain C residue  763 VAL
Chi-restraints excluded: chain C residue  817 VAL
Chi-restraints excluded: chain C residue  923 VAL
Chi-restraints excluded: chain C residue  992 THR
Chi-restraints excluded: chain C residue 1017 ASP
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1113 LEU
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 71 optimal weight:    0.0270
   chunk 20 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 127 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 171 optimal weight:    0.8980
   chunk 145 optimal weight:    0.0670
   chunk 104 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
A 518 ASN
C 610 ASN
F 114 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.149687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.133021 restraints weight = 24163.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 1.87
r_work: 0.3699 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3551 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16844  Z= 0.126
  Angle     :  0.578  14.996  22731  Z= 0.287
  Chirality :  0.038   0.161   2641
  Planarity :  0.004   0.049   2869
  Dihedral  :  3.798  39.947   2224
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.84 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.19), residues: 2032
  helix:  1.67 (0.14), residues: 1424
  sheet: -0.09 (1.10), residues: 24
  loop : -1.75 (0.23), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 191 
 TYR   0.027   0.001   TYR C1117 
 PHE   0.018   0.001   PHE A 566 
 TRP   0.009   0.001   TRP F 213 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (16835)
  covalent geometry    : angle       0.57787 (22731)
  hydrogen bonds       : bond        0.04516 (  965)
  hydrogen bonds       : angle       3.71025 ( 2862)
  metal coordination   : bond        0.00463 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 319
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.6693 (mmt) cc_final: 0.5946 (mmt)
REVERT: A  109 ASP cc_start: 0.6210 (p0) cc_final: 0.5995 (p0)
REVERT: A  143 HIS cc_start: 0.5654 (OUTLIER) cc_final: 0.5316 (m90)
REVERT: A  204 VAL cc_start: 0.7910 (t) cc_final: 0.7519 (m)
REVERT: A  209 VAL cc_start: 0.8477 (p) cc_final: 0.8266 (t)
REVERT: A  247 GLU cc_start: 0.7449 (tp30) cc_final: 0.7217 (tp30)
REVERT: A  250 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7170 (mm-30)
REVERT: A  302 ILE cc_start: 0.7798 (tp) cc_final: 0.7572 (tt)
REVERT: A  472 LYS cc_start: 0.8094 (tppt) cc_final: 0.7815 (ttmm)
REVERT: A  614 TYR cc_start: 0.7660 (m-10) cc_final: 0.7334 (m-10)
REVERT: A  643 LEU cc_start: 0.8037 (mm) cc_final: 0.7824 (mp)
REVERT: A  743 LYS cc_start: 0.7818 (mptt) cc_final: 0.7496 (mptt)
REVERT: B   47 ASN cc_start: 0.8228 (m110) cc_final: 0.8023 (m110)
REVERT: B   50 MET cc_start: 0.7073 (mmm) cc_final: 0.6845 (mmm)
REVERT: B   59 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7456 (p0)
REVERT: C   46 GLU cc_start: 0.7146 (tp30) cc_final: 0.6921 (tp30)
REVERT: C  116 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6859 (tm-30)
REVERT: C  156 ASP cc_start: 0.7753 (m-30) cc_final: 0.7429 (m-30)
REVERT: C  279 PHE cc_start: 0.6597 (t80) cc_final: 0.6330 (t80)
REVERT: C  662 ASN cc_start: 0.8068 (p0) cc_final: 0.7764 (p0)
REVERT: C  691 ASP cc_start: 0.7925 (t0) cc_final: 0.7187 (t0)
REVERT: C  695 ASP cc_start: 0.7616 (m-30) cc_final: 0.7035 (m-30)
REVERT: C  808 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7857 (mtp-110)
REVERT: C  821 PHE cc_start: 0.6696 (m-10) cc_final: 0.6309 (m-10)
REVERT: C  890 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8037 (tp30)
REVERT: C  897 GLN cc_start: 0.7717 (mp10) cc_final: 0.7303 (tm-30)
REVERT: C 1011 PHE cc_start: 0.7483 (m-80) cc_final: 0.7239 (m-80)
REVERT: C 1017 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.5261 (m-30)
REVERT: C 1073 HIS cc_start: 0.7147 (t-90) cc_final: 0.6786 (t-170)
REVERT: C 1106 LEU cc_start: 0.7860 (mp) cc_final: 0.7028 (tt)
REVERT: C 1121 MET cc_start: 0.6632 (mtp) cc_final: 0.6265 (mmm)
REVERT: C 1168 LYS cc_start: 0.7317 (mmmt) cc_final: 0.7049 (mtpp)
REVERT: F  208 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7637 (pp)
  outliers start: 56
  outliers final: 34
  residues processed: 356
  average time/residue: 0.1299
  time to fit residues: 67.8163
Evaluate side-chains
  348 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 310
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  430 SER
Chi-restraints excluded: chain C residue  477 VAL
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  678 ILE
Chi-restraints excluded: chain C residue  763 VAL
Chi-restraints excluded: chain C residue  817 VAL
Chi-restraints excluded: chain C residue  923 VAL
Chi-restraints excluded: chain C residue 1017 ASP
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1068 MET
Chi-restraints excluded: chain C residue 1113 LEU
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 149 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9990
   chunk 138 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 189 optimal weight:    2.9990
   chunk 173 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 201 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A 346 ASN
A 518 ASN
C 847 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.146796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.130230 restraints weight = 24056.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 1.88
r_work: 0.3654 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3503 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16844  Z= 0.173
  Angle     :  0.624  14.200  22731  Z= 0.312
  Chirality :  0.040   0.192   2641
  Planarity :  0.004   0.050   2869
  Dihedral  :  3.946  38.709   2224
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.49 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.19), residues: 2032
  helix:  1.51 (0.14), residues: 1430
  sheet: -0.23 (1.09), residues: 24
  loop : -1.77 (0.23), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 191 
 TYR   0.032   0.002   TYR A 620 
 PHE   0.026   0.002   PHE A 569 
 TRP   0.010   0.001   TRP A 167 
 HIS   0.007   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (16835)
  covalent geometry    : angle       0.62351 (22731)
  hydrogen bonds       : bond        0.05293 (  965)
  hydrogen bonds       : angle       3.86118 ( 2862)
  metal coordination   : bond        0.00732 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 321
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 MET cc_start: 0.6864 (mmt) cc_final: 0.6200 (mmt)
REVERT: A  109 ASP cc_start: 0.6664 (p0) cc_final: 0.6420 (p0)
REVERT: A  143 HIS cc_start: 0.5646 (OUTLIER) cc_final: 0.5382 (m90)
REVERT: A  204 VAL cc_start: 0.7959 (t) cc_final: 0.7573 (m)
REVERT: A  247 GLU cc_start: 0.7539 (tp30) cc_final: 0.7319 (tp30)
REVERT: A  250 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7406 (mm-30)
REVERT: A  302 ILE cc_start: 0.7935 (tp) cc_final: 0.7709 (tt)
REVERT: A  472 LYS cc_start: 0.8085 (tppt) cc_final: 0.7808 (ttmm)
REVERT: A  549 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7490 (mm-40)
REVERT: A  643 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7903 (mp)
REVERT: A  743 LYS cc_start: 0.7688 (mptt) cc_final: 0.7423 (mptt)
REVERT: B   47 ASN cc_start: 0.8270 (m110) cc_final: 0.8048 (m110)
REVERT: B   50 MET cc_start: 0.7161 (mmm) cc_final: 0.6952 (mmm)
REVERT: C   46 GLU cc_start: 0.7172 (tp30) cc_final: 0.6931 (tp30)
REVERT: C  116 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6906 (tm-30)
REVERT: C  156 ASP cc_start: 0.7765 (m-30) cc_final: 0.7417 (m-30)
REVERT: C  279 PHE cc_start: 0.6755 (t80) cc_final: 0.6536 (t80)
REVERT: C  612 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7749 (tt)
REVERT: C  662 ASN cc_start: 0.8131 (p0) cc_final: 0.7823 (p0)
REVERT: C  679 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8402 (mtpp)
REVERT: C  691 ASP cc_start: 0.7942 (t0) cc_final: 0.7230 (t0)
REVERT: C  695 ASP cc_start: 0.7659 (m-30) cc_final: 0.6918 (m-30)
REVERT: C  696 GLU cc_start: 0.6509 (mp0) cc_final: 0.6244 (mp0)
REVERT: C  826 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7450 (mtmm)
REVERT: C  890 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8037 (tp30)
REVERT: C  897 GLN cc_start: 0.7746 (mp10) cc_final: 0.7370 (tm-30)
REVERT: C 1017 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.5491 (m-30)
REVERT: C 1073 HIS cc_start: 0.7172 (t-90) cc_final: 0.6944 (t-170)
REVERT: C 1106 LEU cc_start: 0.7943 (mp) cc_final: 0.7099 (tt)
REVERT: C 1121 MET cc_start: 0.6687 (mtp) cc_final: 0.6346 (mmm)
REVERT: C 1168 LYS cc_start: 0.7411 (mmmt) cc_final: 0.7167 (mtpp)
REVERT: F  116 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7309 (tm-30)
REVERT: F  208 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7696 (pp)
  outliers start: 59
  outliers final: 38
  residues processed: 358
  average time/residue: 0.1346
  time to fit residues: 71.1841
Evaluate side-chains
  357 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 314
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  469 LEU
Chi-restraints excluded: chain C residue  477 VAL
Chi-restraints excluded: chain C residue  612 LEU
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  678 ILE
Chi-restraints excluded: chain C residue  763 VAL
Chi-restraints excluded: chain C residue  923 VAL
Chi-restraints excluded: chain C residue  992 THR
Chi-restraints excluded: chain C residue 1017 ASP
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1068 MET
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 153 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 160 optimal weight:    0.9980
   chunk 137 optimal weight:    0.6980
   chunk 204 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 144 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 114 optimal weight:    0.8980
   chunk 116 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 192 ASN
A 346 ASN
A 518 ASN
B  59 ASN
** C  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.145494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.129083 restraints weight = 24043.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.86
r_work: 0.3636 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16844  Z= 0.178
  Angle     :  0.632  14.807  22731  Z= 0.318
  Chirality :  0.041   0.173   2641
  Planarity :  0.004   0.051   2869
  Dihedral  :  4.029  38.262   2224
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.43 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.19), residues: 2032
  helix:  1.41 (0.14), residues: 1432
  sheet: -0.19 (1.17), residues: 24
  loop : -1.84 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 285 
 TYR   0.026   0.002   TYR C1117 
 PHE   0.019   0.002   PHE A 566 
 TRP   0.012   0.001   TRP F 213 
 HIS   0.007   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (16835)
  covalent geometry    : angle       0.63245 (22731)
  hydrogen bonds       : bond        0.05442 (  965)
  hydrogen bonds       : angle       3.93241 ( 2862)
  metal coordination   : bond        0.00807 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 331
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASP cc_start: 0.7046 (p0) cc_final: 0.6802 (p0)
REVERT: A  121 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7098 (mt0)
REVERT: A  125 ASP cc_start: 0.7612 (m-30) cc_final: 0.7399 (m-30)
REVERT: A  143 HIS cc_start: 0.5570 (OUTLIER) cc_final: 0.5325 (m90)
REVERT: A  173 ARG cc_start: 0.4637 (OUTLIER) cc_final: 0.4325 (mtt180)
REVERT: A  204 VAL cc_start: 0.7949 (t) cc_final: 0.7546 (m)
REVERT: A  247 GLU cc_start: 0.7482 (tp30) cc_final: 0.7268 (tp30)
REVERT: A  302 ILE cc_start: 0.7931 (tp) cc_final: 0.7723 (tt)
REVERT: A  452 VAL cc_start: 0.6982 (OUTLIER) cc_final: 0.6771 (p)
REVERT: A  472 LYS cc_start: 0.8055 (tppt) cc_final: 0.7777 (ttmm)
REVERT: A  643 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: A  743 LYS cc_start: 0.7719 (mptt) cc_final: 0.7485 (mptt)
REVERT: C  116 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6893 (tm-30)
REVERT: C  156 ASP cc_start: 0.7748 (m-30) cc_final: 0.7397 (m-30)
REVERT: C  612 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7859 (tt)
REVERT: C  661 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7580 (ptpp)
REVERT: C  662 ASN cc_start: 0.8153 (p0) cc_final: 0.7835 (p0)
REVERT: C  691 ASP cc_start: 0.7985 (t0) cc_final: 0.7248 (t0)
REVERT: C  695 ASP cc_start: 0.7700 (m-30) cc_final: 0.6911 (m-30)
REVERT: C  696 GLU cc_start: 0.6537 (mp0) cc_final: 0.6250 (mp0)
REVERT: C  748 GLN cc_start: 0.7810 (pp30) cc_final: 0.7548 (pp30)
REVERT: C  826 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7405 (mtmm)
REVERT: C  856 GLU cc_start: 0.6190 (tp30) cc_final: 0.5818 (tp30)
REVERT: C  890 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8115 (tp30)
REVERT: C  897 GLN cc_start: 0.7732 (mp10) cc_final: 0.7363 (tm-30)
REVERT: C  902 GLN cc_start: 0.8039 (mt0) cc_final: 0.7531 (mp10)
REVERT: C  915 GLU cc_start: 0.8426 (mp0) cc_final: 0.8156 (mp0)
REVERT: C  941 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7332 (mp0)
REVERT: C 1017 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.5793 (m-30)
REVERT: C 1106 LEU cc_start: 0.7856 (mp) cc_final: 0.6951 (tt)
REVERT: C 1121 MET cc_start: 0.6678 (mtp) cc_final: 0.6345 (mmm)
REVERT: C 1168 LYS cc_start: 0.7414 (mmmt) cc_final: 0.7176 (mtpp)
REVERT: F  116 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7224 (tm-30)
REVERT: F  208 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7685 (pp)
  outliers start: 63
  outliers final: 40
  residues processed: 369
  average time/residue: 0.1357
  time to fit residues: 73.6804
Evaluate side-chains
  373 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 324
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  469 LEU
Chi-restraints excluded: chain C residue  477 VAL
Chi-restraints excluded: chain C residue  612 LEU
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  678 ILE
Chi-restraints excluded: chain C residue  763 VAL
Chi-restraints excluded: chain C residue  817 VAL
Chi-restraints excluded: chain C residue  923 VAL
Chi-restraints excluded: chain C residue  992 THR
Chi-restraints excluded: chain C residue 1017 ASP
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 117 optimal weight:    0.0980
   chunk 35 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 180 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0010
   chunk 123 optimal weight:    0.6980
   chunk 136 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A 518 ASN
** C  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 247 HIS
C 610 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.146898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130605 restraints weight = 23959.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 1.86
r_work: 0.3654 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3503 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16844  Z= 0.140
  Angle     :  0.620  15.349  22731  Z= 0.308
  Chirality :  0.039   0.191   2641
  Planarity :  0.004   0.051   2869
  Dihedral  :  3.895  39.392   2223
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.05 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.19), residues: 2032
  helix:  1.52 (0.14), residues: 1427
  sheet: -0.13 (1.17), residues: 24
  loop : -1.84 (0.23), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 285 
 TYR   0.023   0.002   TYR C1117 
 PHE   0.025   0.001   PHE F 160 
 TRP   0.010   0.001   TRP F 213 
 HIS   0.008   0.001   HIS C 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (16835)
  covalent geometry    : angle       0.61957 (22731)
  hydrogen bonds       : bond        0.04824 (  965)
  hydrogen bonds       : angle       3.86256 ( 2862)
  metal coordination   : bond        0.00542 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 319
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASP cc_start: 0.7125 (p0) cc_final: 0.6884 (p0)
REVERT: A  143 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.5307 (m90)
REVERT: A  173 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.4199 (ptp-170)
REVERT: A  204 VAL cc_start: 0.7926 (t) cc_final: 0.7508 (m)
REVERT: A  302 ILE cc_start: 0.7921 (tp) cc_final: 0.7703 (tt)
REVERT: A  452 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6724 (p)
REVERT: A  472 LYS cc_start: 0.8064 (tppt) cc_final: 0.7779 (ttmm)
REVERT: A  643 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7891 (mp)
REVERT: A  743 LYS cc_start: 0.7686 (mptt) cc_final: 0.7382 (mptt)
REVERT: B   59 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7297 (p0)
REVERT: C   54 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7862 (mm)
REVERT: C  116 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: C  156 ASP cc_start: 0.7751 (m-30) cc_final: 0.7378 (m-30)
REVERT: C  457 MET cc_start: 0.7603 (tpp) cc_final: 0.7026 (tpp)
REVERT: C  612 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7842 (tt)
REVERT: C  661 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7583 (ptpp)
REVERT: C  662 ASN cc_start: 0.8128 (p0) cc_final: 0.7802 (p0)
REVERT: C  691 ASP cc_start: 0.7959 (t0) cc_final: 0.7237 (t0)
REVERT: C  695 ASP cc_start: 0.7641 (m-30) cc_final: 0.6886 (m-30)
REVERT: C  696 GLU cc_start: 0.6533 (mp0) cc_final: 0.6235 (mp0)
REVERT: C  748 GLN cc_start: 0.7799 (pp30) cc_final: 0.7537 (pp30)
REVERT: C  826 LYS cc_start: 0.7618 (mtpp) cc_final: 0.7372 (mtmm)
REVERT: C  890 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8015 (tp30)
REVERT: C  897 GLN cc_start: 0.7725 (mp10) cc_final: 0.7326 (tm-30)
REVERT: C  941 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7329 (mp0)
REVERT: C 1106 LEU cc_start: 0.7826 (mp) cc_final: 0.6918 (tt)
REVERT: C 1121 MET cc_start: 0.6630 (mtp) cc_final: 0.6326 (mmm)
REVERT: C 1168 LYS cc_start: 0.7389 (mmmt) cc_final: 0.7149 (mtpp)
REVERT: F  116 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7193 (tm-30)
REVERT: F  208 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7655 (pp)
  outliers start: 47
  outliers final: 36
  residues processed: 350
  average time/residue: 0.1408
  time to fit residues: 72.6037
Evaluate side-chains
  361 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 316
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  469 LEU
Chi-restraints excluded: chain C residue  477 VAL
Chi-restraints excluded: chain C residue  612 LEU
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  678 ILE
Chi-restraints excluded: chain C residue  763 VAL
Chi-restraints excluded: chain C residue  817 VAL
Chi-restraints excluded: chain C residue  923 VAL
Chi-restraints excluded: chain C residue  992 THR
Chi-restraints excluded: chain C residue 1017 ASP
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 200 optimal weight:    0.0270
   chunk 175 optimal weight:    0.9990
   chunk 184 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 163 optimal weight:    0.0870
   chunk 171 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 136 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 133 optimal weight:    0.7980
   chunk 143 optimal weight:    0.9990
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
A 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.147445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.131296 restraints weight = 24007.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.85
r_work: 0.3675 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.4720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16844  Z= 0.134
  Angle     :  0.621  15.267  22731  Z= 0.309
  Chirality :  0.039   0.198   2641
  Planarity :  0.004   0.051   2869
  Dihedral  :  3.834  39.091   2223
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.64 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.19), residues: 2032
  helix:  1.56 (0.14), residues: 1430
  sheet:  0.01 (1.17), residues: 24
  loop : -1.83 (0.23), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 285 
 TYR   0.023   0.001   TYR C1117 
 PHE   0.027   0.001   PHE C 482 
 TRP   0.010   0.001   TRP F 213 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (16835)
  covalent geometry    : angle       0.62122 (22731)
  hydrogen bonds       : bond        0.04466 (  965)
  hydrogen bonds       : angle       3.80396 ( 2862)
  metal coordination   : bond        0.00472 (    9)

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

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

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4064 Ramachandran restraints generated.
    2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 325
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASP cc_start: 0.7187 (p0) cc_final: 0.6917 (p0)
REVERT: A  143 HIS cc_start: 0.5526 (OUTLIER) cc_final: 0.5277 (m90)
REVERT: A  204 VAL cc_start: 0.7905 (t) cc_final: 0.7475 (m)
REVERT: A  250 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7364 (mm-30)
REVERT: A  302 ILE cc_start: 0.7910 (tp) cc_final: 0.7699 (tt)
REVERT: A  452 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6698 (p)
REVERT: A  472 LYS cc_start: 0.8028 (tppt) cc_final: 0.7744 (ttmm)
REVERT: A  643 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7871 (mp)
REVERT: A  694 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7258 (mm110)
REVERT: A  697 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7234 (mp0)
REVERT: A  743 LYS cc_start: 0.7679 (mptt) cc_final: 0.7373 (mptt)
REVERT: C   54 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7851 (mm)
REVERT: C  116 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6842 (tm-30)
REVERT: C  156 ASP cc_start: 0.7735 (m-30) cc_final: 0.7356 (m-30)
REVERT: C  457 MET cc_start: 0.7603 (tpp) cc_final: 0.6993 (tpp)
REVERT: C  612 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7819 (tt)
REVERT: C  661 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7583 (ptpp)
REVERT: C  662 ASN cc_start: 0.8129 (p0) cc_final: 0.7792 (p0)
REVERT: C  691 ASP cc_start: 0.7878 (t0) cc_final: 0.7298 (t0)
REVERT: C  695 ASP cc_start: 0.7622 (m-30) cc_final: 0.6950 (m-30)
REVERT: C  696 GLU cc_start: 0.6523 (mp0) cc_final: 0.6259 (mp0)
REVERT: C  826 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7393 (mtmm)
REVERT: C  890 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8100 (tp30)
REVERT: C  897 GLN cc_start: 0.7720 (mp10) cc_final: 0.7334 (tm-30)
REVERT: C  941 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7297 (mp0)
REVERT: C 1106 LEU cc_start: 0.7799 (mp) cc_final: 0.6871 (tt)
REVERT: C 1121 MET cc_start: 0.6609 (mtp) cc_final: 0.6306 (mmm)
REVERT: C 1166 PHE cc_start: 0.7407 (m-80) cc_final: 0.7098 (m-80)
REVERT: C 1168 LYS cc_start: 0.7395 (mmmt) cc_final: 0.7156 (mtpp)
REVERT: F  116 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7154 (tm-30)
REVERT: F  208 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7642 (pp)
  outliers start: 44
  outliers final: 29
  residues processed: 353
  average time/residue: 0.1382
  time to fit residues: 72.2922
Evaluate side-chains
  353 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 316
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 MET
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  509 GLN
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  304 TYR
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  477 VAL
Chi-restraints excluded: chain C residue  612 LEU
Chi-restraints excluded: chain C residue  661 LYS
Chi-restraints excluded: chain C residue  678 ILE
Chi-restraints excluded: chain C residue  763 VAL
Chi-restraints excluded: chain C residue  817 VAL
Chi-restraints excluded: chain C residue  992 THR
Chi-restraints excluded: chain C residue 1017 ASP
Chi-restraints excluded: chain C residue 1052 LEU
Chi-restraints excluded: chain C residue 1058 VAL
Chi-restraints excluded: chain C residue 1119 ILE
Chi-restraints excluded: chain F residue  192 PHE
Chi-restraints excluded: chain F residue  208 ILE
Chi-restraints excluded: chain F residue  231 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 197 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 112 optimal weight:    0.0040
   chunk 203 optimal weight:    0.0670
   chunk 120 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 202 optimal weight:    0.9980
   overall best weight:    0.3330

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

Flipped N/Q/H residues before XYZ refinement:
A 518 ASN
B  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.148565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.132229 restraints weight = 23990.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 1.87
r_work: 0.3684 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16844  Z= 0.129
  Angle     :  0.624  15.000  22731  Z= 0.309
  Chirality :  0.038   0.251   2641
  Planarity :  0.004   0.051   2869
  Dihedral  :  3.803  38.483   2223
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.74 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.19), residues: 2032
  helix:  1.60 (0.14), residues: 1432
  sheet:  0.16 (1.16), residues: 24
  loop : -1.76 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 285 
 TYR   0.027   0.001   TYR C 797 
 PHE   0.026   0.001   PHE C 482 
 TRP   0.009   0.001   TRP F 213 
 HIS   0.003   0.001   HIS C 911 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (16835)
  covalent geometry    : angle       0.62413 (22731)
  hydrogen bonds       : bond        0.04248 (  965)
  hydrogen bonds       : angle       3.77975 ( 2862)
  metal coordination   : bond        0.00395 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4550.06 seconds
wall clock time: 78 minutes 40.63 seconds (4720.63 seconds total)