Starting phenix.real_space_refine
on Fri Jul  3 13:43:35 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8g7u_29824/07_2026/8g7u_29824.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      52      5.49       5
     S      80      5.16       5
     C    8895      2.51       5
     N    2424      2.21       5
     O    2776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14229
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 647, 5234
          Classifications: {'peptide': 647}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 619}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1424
          Classifications: {'peptide': 178}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 170}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 5115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 631, 5115
          Classifications: {'peptide': 631}
          Link IDs: {'PTRANS': 27, 'TRANS': 603}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1415
          Classifications: {'peptide': 178}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 7, 'TRANS': 170}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
    Chain: "X"
      Number of atoms: 523
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 523
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 23, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 22, None: 1}
            Not linked:
              pdbres="GTP X   1 "
              pdbres="  G X   2 "
    Chain: "Y"
      Number of atoms: 516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 516
          Unusual residues: {'UTP': 1}
          Classifications: {'RNA': 23, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12}
          Link IDs: {'rna3p': 22, None: 1}
            Not linked:
              pdbres="UTP Y   1 "
              pdbres="  C Y   2 "
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4328  SG  CYS A 813      90.632  21.520  41.450  1.00 83.84           S
  ATOM   4741  SG  CYS A 864      87.352  22.632  37.635  1.00106.15           S
  ATOM  10849  SG  CYS C 810     103.431  77.672  58.361  1.00 20.23           S
  ATOM  11288  SG  CYS C 864     105.544  81.022  58.252  1.00 52.52           S
  ATOM  11327  SG  CYS C 869     102.103  80.659  56.989  1.00 44.16           S

  Time building chain proxies: 3.17, per 1000 atoms: 0.22
  Number of scatterers: 14229
  At special positions: 0
  Unit cell: (130.045, 117.46, 127.528, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      80     16.00
     P      52     15.00
     O    2776      8.00
     N    2424      7.00
     C    8895      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 347 " - pdb=" SG  CYS B 402 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 347 " - pdb=" SG  CYS D 402 " distance=2.04

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 623.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 813 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
      pdb="  ZN C1001 "
        pdb="ZN    ZN C1001 " - pdb=" SG  CYS C 869 "
        pdb="ZN    ZN C1001 " - pdb=" SG  CYS C 810 "
        pdb="ZN    ZN C1001 " - pdb=" SG  CYS C 864 "


  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3128

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 15 sheets defined
      38.6% alpha, 11.3% beta
      13 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 255
      removed outlier: 5.188A  pdb=" N   LEU A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 267 through 284
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 325 through 329
    Processing helix  chain 'A' and resid 333 through 340
      removed outlier: 4.008A  pdb=" N   ILE A 337 " --> pdb=" O   PRO A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.723A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.748A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 377
    Processing helix  chain 'A' and resid 381 through 395
    Processing helix  chain 'A' and resid 419 through 433
    Processing helix  chain 'A' and resid 445 through 452
      removed outlier: 3.907A  pdb=" N   VAL A 452 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 487
      removed outlier: 3.542A  pdb=" N   LYS A 487 " --> pdb=" O   GLU A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 506 through 521
    Processing helix  chain 'A' and resid 529 through 558
    Processing helix  chain 'A' and resid 559 through 578
      removed outlier: 3.663A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A 577 " --> pdb=" O   ASN A 573 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLY A 578 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 601
      removed outlier: 4.155A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 607
      removed outlier: 6.118A  pdb=" N   SER A 605 " --> pdb=" O   ARG A 602 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU A 607 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 637 through 648
      removed outlier: 4.064A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 769
      removed outlier: 4.322A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 794
    Processing helix  chain 'A' and resid 837 through 840
    Processing helix  chain 'A' and resid 889 through 892
    Processing helix  chain 'A' and resid 907 through 911
    Processing helix  chain 'C' and resid 245 through 250
    Processing helix  chain 'C' and resid 251 through 256
    Processing helix  chain 'C' and resid 268 through 283
      removed outlier: 3.836A  pdb=" N   LEU C 275 " --> pdb=" O   THR C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 315
      removed outlier: 3.576A  pdb=" N   PHE C 314 " --> pdb=" O   PHE C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 338
    Processing helix  chain 'C' and resid 348 through 357
    Processing helix  chain 'C' and resid 362 through 366
      removed outlier: 3.861A  pdb=" N   ILE C 365 " --> pdb=" O   SER C 362 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 374 through 377
    Processing helix  chain 'C' and resid 381 through 395
    Processing helix  chain 'C' and resid 419 through 434
    Processing helix  chain 'C' and resid 445 through 450
    Processing helix  chain 'C' and resid 469 through 491
    Processing helix  chain 'C' and resid 492 through 496
    Processing helix  chain 'C' and resid 506 through 521
      removed outlier: 3.900A  pdb=" N   GLU C 510 " --> pdb=" O   THR C 506 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 527 through 556
      removed outlier: 3.890A  pdb=" N   ARG C 533 " --> pdb=" O   ASP C 529 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 576
      removed outlier: 4.041A  pdb=" N   ALA C 563 " --> pdb=" O   ARG C 559 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 580 through 602
      removed outlier: 3.905A  pdb=" N   LYS C 593 " --> pdb=" O   ARG C 589 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   GLN C 595 " --> pdb=" O   GLU C 591 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   GLU C 596 " --> pdb=" O   GLU C 592 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 608 through 625
      removed outlier: 3.717A  pdb=" N   LEU C 624 " --> pdb=" O   GLU C 620 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 637 through 649
    Processing helix  chain 'C' and resid 746 through 769
    Processing helix  chain 'C' and resid 772 through 792
    Processing helix  chain 'C' and resid 836 through 840
      removed outlier: 3.732A  pdb=" N   GLU C 840 " --> pdb=" O   ALA C 837 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 263
      removed outlier: 6.129A  pdb=" N   ILE A 262 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LEU A 408 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL A 294 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   ASP A 372 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   PHE A 296 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 344 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 462
      removed outlier: 6.495A  pdb=" N   VAL A 712 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   LEU A 741 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   LEU A 714 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   VAL A 634 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819
      removed outlier: 3.942A  pdb=" N   CYS A 818 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833
      removed outlier: 4.630A  pdb=" N   ILE A 916 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846
      removed outlier: 4.174A  pdb=" N   ILE A 862 " --> pdb=" O   GLY A 874 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 280 through 282
      removed outlier: 3.777A  pdb=" N   ILE B 426 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 302
      removed outlier: 3.670A  pdb=" N   GLY B 328 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   TRP B 325 " --> pdb=" O   TRP B 351 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   TRP B 351 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL B 327 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 261 through 262
      removed outlier: 6.552A  pdb=" N   VAL C 294 " --> pdb=" O   ILE C 370 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   ASP C 372 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   PHE C 296 " --> pdb=" O   ASP C 372 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 457 through 458
      removed outlier: 6.822A  pdb=" N   GLN C 457 " --> pdb=" O   CYS C 738 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 461 through 462
      removed outlier: 3.915A  pdb=" N   THR C 742 " --> pdb=" O   ARG C 461 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU C 714 " --> pdb=" O   LEU C 741 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 659 through 660
      removed outlier: 6.847A  pdb=" N   GLY C 659 " --> pdb=" O   ILE C 695 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 816 through 819
      removed outlier: 6.723A  pdb=" N   LEU C 808 " --> pdb=" O   ALA C 817 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   TYR C 819 " --> pdb=" O   LYS C 806 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LYS C 806 " --> pdb=" O   TYR C 819 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU C 809 " --> pdb=" O   VAL C 893 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 823 through 825
      removed outlier: 4.527A  pdb=" N   TYR C 831 " --> pdb=" O   ILE C 887 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL C 833 " --> pdb=" O   PRO C 885 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ASP C 872 " --> pdb=" O   CYS C 864 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   CYS C 864 " --> pdb=" O   ASP C 872 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY C 874 " --> pdb=" O   ILE C 862 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LYS C 878 " --> pdb=" O   LYS C 858 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   LYS C 858 " --> pdb=" O   LYS C 878 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS C 861 " --> pdb=" O   ARG C 845 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 280 through 282
    Processing sheet with id=AB6, first strand: chain 'D' and resid 301 through 303
      removed outlier: 4.271A  pdb=" N   TRP D 325 " --> pdb=" O   TRP D 351 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   CYS D 347 " --> pdb=" O   VAL D 329 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   CYS D 348 " --> pdb=" O   TRP D 360 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      31 hydrogen bonds
      62 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 2223
        1.29 -     1.43: 4050
        1.43 -     1.56: 8152
        1.56 -     1.69: 106
        1.69 -     1.82: 108
  Bond restraints: 14639
  Sorted by residual:
  bond pdb=" C1' GTP X   1 "
       pdb=" C2' GTP X   1 "
    ideal  model  delta    sigma   weight residual
    1.524  1.286  0.238 2.00e-02 2.50e+03 1.41e+02
  bond pdb=" C3' UTP Y   1 "
       pdb=" C4' UTP Y   1 "
    ideal  model  delta    sigma   weight residual
    1.527  1.303  0.224 2.00e-02 2.50e+03 1.25e+02
  bond pdb=" C1' GTP X   1 "
       pdb=" O4' GTP X   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.613 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C1' UTP Y   1 "
       pdb=" C2' UTP Y   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.333  0.192 2.00e-02 2.50e+03 9.22e+01
  bond pdb=" C5  GTP X   1 "
       pdb=" C6  GTP X   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.544 -0.154 2.00e-02 2.50e+03 5.96e+01
  ... (remaining 14634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 19362
        2.39 -     4.78: 554
        4.78 -     7.17: 70
        7.17 -     9.57: 13
        9.57 -    11.96: 8
  Bond angle restraints: 20007
  Sorted by residual:
  angle pdb=" CA  VAL C 332 "
        pdb=" CB  VAL C 332 "
        pdb=" CG1 VAL C 332 "
      ideal   model   delta    sigma   weight residual
     110.40  117.42   -7.02 1.70e+00 3.46e-01 1.70e+01
  angle pdb=" C   ASP A 527 "
        pdb=" N   LYS A 528 "
        pdb=" CA  LYS A 528 "
      ideal   model   delta    sigma   weight residual
     121.54  129.33   -7.79 1.91e+00 2.74e-01 1.66e+01
  angle pdb=" O1A UTP Y   1 "
        pdb=" PA  UTP Y   1 "
        pdb=" O2A UTP Y   1 "
      ideal   model   delta    sigma   weight residual
     121.55  109.59   11.96 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C   GLN B 395 "
        pdb=" N   GLU B 396 "
        pdb=" CA  GLU B 396 "
      ideal   model   delta    sigma   weight residual
     122.46  127.73   -5.27 1.41e+00 5.03e-01 1.40e+01
  angle pdb=" O3A UTP Y   1 "
        pdb=" PB  UTP Y   1 "
        pdb=" O3B UTP Y   1 "
      ideal   model   delta    sigma   weight residual
      98.89  109.60  -10.71 3.00e+00 1.11e-01 1.27e+01
  ... (remaining 20002 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 7645
       17.94 -    35.88: 914
       35.88 -    53.82: 165
       53.82 -    71.76: 33
       71.76 -    89.71: 17
  Dihedral angle restraints: 8774
    sinusoidal: 3968
      harmonic: 4806
  Sorted by residual:
  dihedral pdb=" CA  SER A 855 "
           pdb=" C   SER A 855 "
           pdb=" N   PHE A 856 "
           pdb=" CA  PHE A 856 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.55  -29.45     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  THR C 347 "
           pdb=" C   THR C 347 "
           pdb=" N   PRO C 348 "
           pdb=" CA  PRO C 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.95  -29.05     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  PHE A 856 "
           pdb=" C   PHE A 856 "
           pdb=" N   GLU A 857 "
           pdb=" CA  GLU A 857 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.51   27.49     0      5.00e+00 4.00e-02 3.02e+01
  ... (remaining 8771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1649
       0.057 -    0.115: 460
       0.115 -    0.172: 113
       0.172 -    0.230: 17
       0.230 -    0.287: 5
  Chirality restraints: 2244
  Sorted by residual:
  chirality pdb=" CB  VAL A 522 "
            pdb=" CA  VAL A 522 "
            pdb=" CG1 VAL A 522 "
            pdb=" CG2 VAL A 522 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CB  VAL C 332 "
            pdb=" CA  VAL C 332 "
            pdb=" CG1 VAL C 332 "
            pdb=" CG2 VAL C 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C3' UTP Y   1 "
            pdb=" C2' UTP Y   1 "
            pdb=" C4' UTP Y   1 "
            pdb=" O3' UTP Y   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.69   -2.44   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 2241 not shown)

  Planarity restraints: 2362
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 261 "    0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   ILE A 261 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   ILE A 261 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE A 262 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 381 "    0.055 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO C 382 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO C 382 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 382 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 286 "   -0.044 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO D 287 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 287 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 287 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2359 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 189
        2.62 -     3.19: 11819
        3.19 -     3.76: 22936
        3.76 -     4.33: 29317
        4.33 -     4.90: 47100
  Nonbonded interactions: 111361
  Sorted by model distance:
  nonbonded pdb=" O2' UTP Y   1 "
            pdb=" OP2   C Y   2 "
     model   vdw
     2.056 3.040
  nonbonded pdb=" C3' GTP X   1 "
            pdb=" OP2   G X   2 "
     model   vdw
     2.058 2.776
  nonbonded pdb=" O2' UTP Y   1 "
            pdb=" P     C Y   2 "
     model   vdw
     2.068 3.400
  nonbonded pdb=" OG  SER C 698 "
            pdb=" OH  TYR C 717 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER C 855 "
            pdb=" OG  SER C 855 "
     model   vdw
     2.288 3.040
  ... (remaining 111356 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 241 through 661 or resid 690 through 699 or resid 709 thro \ 
ugh 718 or resid 734 through 922 or resid 1001))
  selection = (chain 'C' and resid 241 through 1001)
}
ncs_group {
  reference = (chain 'B' and (resid 252 through 343 or (resid 344 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 345 through 360 or resid 364 through 430)) \ 

  selection = (chain 'D' and (resid 252 through 360 or resid 364 through 430))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     16.290
  Find NCS groups from input model:        0.330
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
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      :  0.010   0.400  14648  Z= 0.430
  Angle     :  0.978  11.958  20011  Z= 0.520
  Chirality :  0.057   0.287   2244
  Planarity :  0.007   0.083   2362
  Dihedral  : 15.884  89.706   5640
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 12.24 %
    Favored  : 87.15 %
  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 are not related in a simple way.
  whole: -3.99 (0.17), residues: 1610
  helix: -1.95 (0.16), residues: 584
  sheet: -2.69 (0.29), residues: 288
  loop : -3.18 (0.19), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 559 
 TYR   0.019   0.002   TYR D 400 
 PHE   0.029   0.003   PHE A 842 
 TRP   0.017   0.002   TRP C 908 
 HIS   0.012   0.002   HIS C 847 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00841 /  0.40 (14639)
  covalent geometry    : angle       0.97823 /  0.52 (20007)
  SS BOND              : bond        0.00935 /  0.45 (    2)
  SS BOND              : angle       0.93874 /  0.53 (    4)
  hydrogen bonds       : bond        0.16225 / 10.73 (  563)
  hydrogen bonds       : angle       7.39294 /  5.07 ( 1592)
  metal coordination   : bond        0.24235 / 11.95 (    5)
  Misc. bond           : bond        0.05378 /  2.71 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 216
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 ILE cc_start: 0.7695 (mp) cc_final: 0.7262 (mp)
REVERT: A  760 MET cc_start: 0.4704 (ppp) cc_final: 0.3432 (ppp)
REVERT: B  324 HIS cc_start: 0.6566 (m-70) cc_final: 0.6107 (m-70)
REVERT: D  277 ASP cc_start: 0.8343 (p0) cc_final: 0.8142 (p0)
REVERT: D  379 TRP cc_start: 0.7373 (t60) cc_final: 0.6871 (t60)
REVERT: D  411 TYR cc_start: 0.8320 (m-80) cc_final: 0.8074 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 224
  average time/residue: 0.1433
  time to fit residues: 45.1094
Evaluate side-chains
  142 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain D residue  363 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:   40.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    1.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 287 GLN
A 305 GLN
A 389 ASN
A 606 ASN
A 752 GLN
B 256 GLN
B 324 HIS
B 429 GLN
C 259 ASN
C 287 GLN
C 306 GLN
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 511 GLN
C 619 GLN
C 769 GLN
C 830 HIS
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 ASN
** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 423 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.137848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.113649 restraints weight = 37901.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.115366 restraints weight = 45618.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.115695 restraints weight = 34041.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.116013 restraints weight = 21098.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.116530 restraints weight = 19702.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14648  Z= 0.144
  Angle     :  0.624  11.793  20011  Z= 0.321
  Chirality :  0.042   0.195   2244
  Planarity :  0.005   0.060   2362
  Dihedral  :  8.812  85.862   2350
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.59 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.20), residues: 1610
  helix:  0.03 (0.20), residues: 587
  sheet: -2.53 (0.29), residues: 276
  loop : -2.84 (0.20), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 480 
 TYR   0.017   0.001   TYR C 426 
 PHE   0.012   0.001   PHE A 853 
 TRP   0.015   0.001   TRP C 512 
 HIS   0.005   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 (14639)
  covalent geometry    : angle       0.62356 /  0.32 (20007)
  SS BOND              : bond        0.01429 /  0.68 (    2)
  SS BOND              : angle       1.04691 /  0.72 (    4)
  hydrogen bonds       : bond        0.04448 /  2.94 (  563)
  hydrogen bonds       : angle       5.21972 /  3.58 ( 1592)
  metal coordination   : bond        0.00398 /  0.20 (    5)
  Misc. bond           : bond        0.00109 /  0.05 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 174
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.2577 (OUTLIER) cc_final: 0.2020 (tptp)
REVERT: A  525 MET cc_start: 0.5717 (ttt) cc_final: 0.5470 (tmm)
REVERT: A  755 MET cc_start: 0.4308 (tmm) cc_final: 0.3148 (tpt)
REVERT: A  760 MET cc_start: 0.4730 (ppp) cc_final: 0.3746 (ppp)
REVERT: B  324 HIS cc_start: 0.6801 (m90) cc_final: 0.6567 (m90)
REVERT: C  457 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7724 (pt0)
REVERT: C  698 SER cc_start: 0.8092 (m) cc_final: 0.7807 (p)
REVERT: D  277 ASP cc_start: 0.8576 (p0) cc_final: 0.8332 (p0)
REVERT: D  297 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6919 (m-10)
REVERT: D  316 GLU cc_start: 0.6647 (tt0) cc_final: 0.6204 (tt0)
REVERT: D  379 TRP cc_start: 0.7683 (t60) cc_final: 0.7144 (t60)
REVERT: D  428 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6815 (pptt)
  outliers start: 39
  outliers final: 24
  residues processed: 203
  average time/residue: 0.1177
  time to fit residues: 35.1073
Evaluate side-chains
  166 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  525 MET
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  297 PHE
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  375 VAL
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 429 GLN
C 281 HIS
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 868 ASN
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 338 GLN
** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.137172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.114172 restraints weight = 37922.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.114531 restraints weight = 46869.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.115270 restraints weight = 38415.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.115748 restraints weight = 24372.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.116333 restraints weight = 21929.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14648  Z= 0.144
  Angle     :  0.597  11.894  20011  Z= 0.304
  Chirality :  0.042   0.208   2244
  Planarity :  0.004   0.054   2362
  Dihedral  :  8.448  87.783   2350
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.08 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.20), residues: 1610
  helix:  0.71 (0.21), residues: 591
  sheet: -2.33 (0.30), residues: 265
  loop : -2.63 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 811 
 TYR   0.015   0.001   TYR C 548 
 PHE   0.013   0.001   PHE A 739 
 TRP   0.012   0.001   TRP C 512 
 HIS   0.005   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 (14639)
  covalent geometry    : angle       0.59663 /  0.30 (20007)
  SS BOND              : bond        0.00525 /  0.25 (    2)
  SS BOND              : angle       1.59576 /  1.31 (    4)
  hydrogen bonds       : bond        0.04188 /  2.72 (  563)
  hydrogen bonds       : angle       4.91502 /  3.37 ( 1592)
  metal coordination   : bond        0.00388 /  0.19 (    5)
  Misc. bond           : bond        0.00043 /  0.02 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 157
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7752 (mtt)
REVERT: A  434 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8864 (tt)
REVERT: A  462 LYS cc_start: 0.2788 (OUTLIER) cc_final: 0.2011 (tptp)
REVERT: A  521 MET cc_start: 0.7139 (mtp) cc_final: 0.6770 (mtp)
REVERT: A  760 MET cc_start: 0.4814 (ppp) cc_final: 0.3902 (ppp)
REVERT: B  324 HIS cc_start: 0.6701 (m90) cc_final: 0.6404 (m90)
REVERT: C  434 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9206 (mp)
REVERT: C  457 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7801 (pt0)
REVERT: C  523 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7050 (m-80)
REVERT: C  611 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8921 (mp)
REVERT: C  698 SER cc_start: 0.8022 (m) cc_final: 0.7808 (p)
REVERT: C  857 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6875 (mm-30)
REVERT: D  277 ASP cc_start: 0.8467 (p0) cc_final: 0.8240 (p0)
REVERT: D  297 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6802 (m-10)
REVERT: D  316 GLU cc_start: 0.6856 (tt0) cc_final: 0.6312 (tt0)
REVERT: D  338 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8470 (mm110)
REVERT: D  428 LYS cc_start: 0.7423 (pptt) cc_final: 0.6847 (pptt)
  outliers start: 52
  outliers final: 33
  residues processed: 198
  average time/residue: 0.1235
  time to fit residues: 36.2420
Evaluate side-chains
  181 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 140
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  429 GLN
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  441 THR
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  523 PHE
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  836 ASP
Chi-restraints excluded: chain C residue  847 HIS
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  297 PHE
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  375 VAL
Chi-restraints excluded: chain D residue  416 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 45 optimal weight:   20.0000
   chunk 148 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 155 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 121 optimal weight:    0.9990
   chunk 129 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 GLN
C 477 GLN
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.134682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.111151 restraints weight = 38038.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.112718 restraints weight = 44061.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.112662 restraints weight = 37748.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.113550 restraints weight = 23649.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.113709 restraints weight = 20318.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14648  Z= 0.222
  Angle     :  0.665  11.027  20011  Z= 0.338
  Chirality :  0.043   0.214   2244
  Planarity :  0.004   0.056   2362
  Dihedral  :  8.466  84.846   2350
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 18.90 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.21), residues: 1610
  helix:  0.82 (0.21), residues: 591
  sheet: -2.28 (0.30), residues: 264
  loop : -2.47 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 811 
 TYR   0.015   0.002   TYR C 426 
 PHE   0.025   0.002   PHE A 633 
 TRP   0.010   0.001   TRP C 908 
 HIS   0.004   0.001   HIS C 375 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00499 /  0.22 (14639)
  covalent geometry    : angle       0.66424 /  0.34 (20007)
  SS BOND              : bond        0.00603 /  0.29 (    2)
  SS BOND              : angle       1.65428 /  1.35 (    4)
  hydrogen bonds       : bond        0.04481 /  2.93 (  563)
  hydrogen bonds       : angle       5.04223 /  3.45 ( 1592)
  metal coordination   : bond        0.00475 /  0.24 (    5)
  Misc. bond           : bond        0.00054 /  0.03 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 152
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5299 (tp)
REVERT: A  369 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7699 (mtt)
REVERT: A  462 LYS cc_start: 0.2651 (OUTLIER) cc_final: 0.1797 (tptp)
REVERT: A  760 MET cc_start: 0.4819 (ppp) cc_final: 0.3945 (ppp)
REVERT: B  324 HIS cc_start: 0.6720 (m90) cc_final: 0.6430 (m90)
REVERT: B  398 LEU cc_start: 0.0797 (OUTLIER) cc_final: 0.0567 (pp)
REVERT: C  434 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9200 (mp)
REVERT: C  457 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7764 (pt0)
REVERT: C  698 SER cc_start: 0.8209 (m) cc_final: 0.7986 (p)
REVERT: D  277 ASP cc_start: 0.8413 (p0) cc_final: 0.8196 (p0)
REVERT: D  316 GLU cc_start: 0.6992 (tt0) cc_final: 0.6421 (tt0)
REVERT: D  337 ASP cc_start: 0.8377 (p0) cc_final: 0.8162 (p0)
REVERT: D  338 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8712 (tp40)
REVERT: D  379 TRP cc_start: 0.7797 (t60) cc_final: 0.6768 (t60)
REVERT: D  428 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6550 (pptt)
  outliers start: 71
  outliers final: 50
  residues processed: 209
  average time/residue: 0.1185
  time to fit residues: 37.1007
Evaluate side-chains
  192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 135
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  888 LYS
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  259 ASN
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  441 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  498 GLN
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain C residue  753 ILE
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  836 ASP
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  260 HIS
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  273 GLU
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  375 VAL
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 144 optimal weight:    0.4980
   chunk 32 optimal weight:    8.9990
   chunk 145 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 117 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 133 optimal weight:    9.9990
   chunk 101 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   overall best weight:    2.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 557 HIS
B 321 ASN
** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.135881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.112688 restraints weight = 37752.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.114138 restraints weight = 44671.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.114246 restraints weight = 37524.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.114780 restraints weight = 23830.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.115549 restraints weight = 20937.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14648  Z= 0.165
  Angle     :  0.614   9.846  20011  Z= 0.311
  Chirality :  0.042   0.181   2244
  Planarity :  0.004   0.054   2362
  Dihedral  :  8.267  85.649   2350
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 19.03 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.21), residues: 1610
  helix:  1.04 (0.21), residues: 591
  sheet: -2.11 (0.31), residues: 255
  loop : -2.41 (0.22), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 811 
 TYR   0.014   0.001   TYR C 548 
 PHE   0.019   0.001   PHE A 633 
 TRP   0.012   0.001   TRP C 512 
 HIS   0.003   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 (14639)
  covalent geometry    : angle       0.61382 /  0.31 (20007)
  SS BOND              : bond        0.00473 /  0.23 (    2)
  SS BOND              : angle       1.33116 /  1.08 (    4)
  hydrogen bonds       : bond        0.04133 /  2.68 (  563)
  hydrogen bonds       : angle       4.84865 /  3.31 ( 1592)
  metal coordination   : bond        0.00378 /  0.19 (    5)
  Misc. bond           : bond        0.00040 /  0.02 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 150
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5253 (tp)
REVERT: A  369 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7640 (mtt)
REVERT: A  462 LYS cc_start: 0.2639 (OUTLIER) cc_final: 0.1879 (tptp)
REVERT: A  711 LEU cc_start: 0.6280 (mt) cc_final: 0.5900 (mt)
REVERT: A  760 MET cc_start: 0.4797 (ppp) cc_final: 0.3911 (ppp)
REVERT: B  324 HIS cc_start: 0.6795 (m90) cc_final: 0.6524 (m90)
REVERT: B  420 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7203 (t-90)
REVERT: C  434 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9216 (mp)
REVERT: C  457 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7752 (pt0)
REVERT: C  698 SER cc_start: 0.8080 (m) cc_final: 0.7874 (p)
REVERT: D  277 ASP cc_start: 0.8447 (p0) cc_final: 0.8223 (p0)
REVERT: D  338 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8619 (tp40)
REVERT: D  379 TRP cc_start: 0.7767 (t60) cc_final: 0.6791 (t60)
  outliers start: 75
  outliers final: 54
  residues processed: 206
  average time/residue: 0.1137
  time to fit residues: 35.4570
Evaluate side-chains
  200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 140
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  888 LYS
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  259 ASN
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  441 THR
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  498 GLN
Chi-restraints excluded: chain C residue  516 VAL
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  836 ASP
Chi-restraints excluded: chain C residue  847 HIS
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  260 HIS
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  345 ASP
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  375 VAL
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 143 optimal weight:   10.0000
   chunk 132 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 134 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   chunk 78 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 507 GLN
A 549 ASN
A 623 HIS
** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 393 GLN
C 511 GLN
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.139206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.118684 restraints weight = 37926.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.119100 restraints weight = 45726.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.119363 restraints weight = 39020.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.119826 restraints weight = 26015.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.120243 restraints weight = 22500.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14648  Z= 0.104
  Angle     :  0.575  11.054  20011  Z= 0.288
  Chirality :  0.041   0.196   2244
  Planarity :  0.004   0.052   2362
  Dihedral  :  7.967  87.232   2350
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 20.80 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.21), residues: 1610
  helix:  1.42 (0.21), residues: 589
  sheet: -1.98 (0.31), residues: 259
  loop : -2.28 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 502 
 TYR   0.017   0.001   TYR C 548 
 PHE   0.012   0.001   PHE A 633 
 TRP   0.020   0.001   TRP C 512 
 HIS   0.004   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.10 (14639)
  covalent geometry    : angle       0.57484 /  0.29 (20007)
  SS BOND              : bond        0.00273 /  0.13 (    2)
  SS BOND              : angle       0.91915 /  0.66 (    4)
  hydrogen bonds       : bond        0.03656 /  2.38 (  563)
  hydrogen bonds       : angle       4.48397 /  3.06 ( 1592)
  metal coordination   : bond        0.00285 /  0.14 (    5)
  Misc. bond           : bond        0.00033 /  0.02 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 174
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5522 (OUTLIER) cc_final: 0.5248 (tp)
REVERT: A  266 THR cc_start: 0.5343 (OUTLIER) cc_final: 0.4793 (p)
REVERT: A  369 MET cc_start: 0.8005 (mmm) cc_final: 0.7265 (mtt)
REVERT: A  462 LYS cc_start: 0.2633 (OUTLIER) cc_final: 0.2170 (tptp)
REVERT: A  525 MET cc_start: 0.5390 (tmm) cc_final: 0.5145 (tmm)
REVERT: A  711 LEU cc_start: 0.6177 (mt) cc_final: 0.5868 (mt)
REVERT: A  760 MET cc_start: 0.4762 (ppp) cc_final: 0.3911 (ppp)
REVERT: A  772 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6590 (m-30)
REVERT: C  611 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8838 (mp)
REVERT: D  277 ASP cc_start: 0.8345 (p0) cc_final: 0.8102 (p0)
REVERT: D  299 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8895 (m)
REVERT: D  338 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8437 (mm110)
  outliers start: 54
  outliers final: 32
  residues processed: 213
  average time/residue: 0.1123
  time to fit residues: 36.2619
Evaluate side-chains
  185 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 147
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  557 HIS
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  410 LEU
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 152 optimal weight:    3.9990
   chunk 146 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 131 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 429 GLN
C 495 ASN
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.138507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.115824 restraints weight = 37734.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.116383 restraints weight = 48506.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.117177 restraints weight = 38760.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.117622 restraints weight = 25337.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.118177 restraints weight = 22526.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14648  Z= 0.122
  Angle     :  0.592  11.177  20011  Z= 0.297
  Chirality :  0.041   0.177   2244
  Planarity :  0.004   0.049   2362
  Dihedral  :  7.857  85.101   2349
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 20.60 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.21), residues: 1610
  helix:  1.48 (0.21), residues: 590
  sheet: -1.88 (0.32), residues: 252
  loop : -2.23 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 824 
 TYR   0.017   0.001   TYR C 548 
 PHE   0.013   0.001   PHE A 739 
 TRP   0.016   0.001   TRP C 512 
 HIS   0.004   0.001   HIS D 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 (14639)
  covalent geometry    : angle       0.59180 /  0.30 (20007)
  SS BOND              : bond        0.00365 /  0.18 (    2)
  SS BOND              : angle       1.07054 /  0.79 (    4)
  hydrogen bonds       : bond        0.03741 /  2.43 (  563)
  hydrogen bonds       : angle       4.43946 /  3.02 ( 1592)
  metal coordination   : bond        0.00324 /  0.16 (    5)
  Misc. bond           : bond        0.00027 /  0.01 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 155
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5547 (OUTLIER) cc_final: 0.5237 (tp)
REVERT: A  266 THR cc_start: 0.5504 (OUTLIER) cc_final: 0.5031 (p)
REVERT: A  369 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7534 (mtt)
REVERT: A  525 MET cc_start: 0.5428 (tmm) cc_final: 0.5122 (tmm)
REVERT: A  711 LEU cc_start: 0.6138 (mt) cc_final: 0.5840 (mt)
REVERT: A  760 MET cc_start: 0.4878 (ppp) cc_final: 0.4058 (ppp)
REVERT: A  772 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6713 (m-30)
REVERT: B  420 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7236 (t-90)
REVERT: C  434 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9283 (mp)
REVERT: C  611 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8839 (mp)
REVERT: D  277 ASP cc_start: 0.8322 (p0) cc_final: 0.8120 (p0)
REVERT: D  338 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8456 (mm110)
  outliers start: 64
  outliers final: 44
  residues processed: 202
  average time/residue: 0.1128
  time to fit residues: 34.7626
Evaluate side-chains
  197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 146
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  557 HIS
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  429 GLN
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  495 ASN
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  847 HIS
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  260 HIS
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  273 GLU
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 132 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0970
   chunk 64 optimal weight:    5.9990
   chunk 71 optimal weight:   40.0000
   chunk 32 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0170
   chunk 52 optimal weight:   30.0000
   overall best weight:    1.1420

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
D 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.139417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.117590 restraints weight = 37819.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.117587 restraints weight = 48592.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.118338 restraints weight = 41655.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.119259 restraints weight = 26095.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.119559 restraints weight = 23009.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14648  Z= 0.111
  Angle     :  0.589  13.320  20011  Z= 0.293
  Chirality :  0.041   0.201   2244
  Planarity :  0.004   0.049   2362
  Dihedral  :  7.838  85.715   2349
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 21.62 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.22), residues: 1610
  helix:  1.61 (0.21), residues: 584
  sheet: -1.85 (0.32), residues: 255
  loop : -2.11 (0.23), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 824 
 TYR   0.023   0.001   TYR C 548 
 PHE   0.014   0.001   PHE A 571 
 TRP   0.016   0.001   TRP C 512 
 HIS   0.003   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 (14639)
  covalent geometry    : angle       0.58840 /  0.29 (20007)
  SS BOND              : bond        0.00328 /  0.16 (    2)
  SS BOND              : angle       1.08004 /  0.75 (    4)
  hydrogen bonds       : bond        0.03672 /  2.38 (  563)
  hydrogen bonds       : angle       4.38181 /  2.99 ( 1592)
  metal coordination   : bond        0.00208 /  0.10 (    5)
  Misc. bond           : bond        0.00024 /  0.01 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 156
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5212 (tp)
REVERT: A  266 THR cc_start: 0.5338 (OUTLIER) cc_final: 0.4852 (p)
REVERT: A  369 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7488 (mtt)
REVERT: A  465 SER cc_start: 0.8986 (t) cc_final: 0.8270 (m)
REVERT: A  711 LEU cc_start: 0.6098 (mt) cc_final: 0.5807 (mt)
REVERT: A  760 MET cc_start: 0.4856 (ppp) cc_final: 0.4150 (ppp)
REVERT: A  772 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6696 (m-30)
REVERT: B  420 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7303 (t-90)
REVERT: C  434 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9258 (mp)
REVERT: C  457 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7852 (pt0)
REVERT: C  611 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8838 (mp)
REVERT: D  277 ASP cc_start: 0.8337 (p0) cc_final: 0.8123 (p0)
REVERT: D  338 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8428 (mm110)
  outliers start: 59
  outliers final: 43
  residues processed: 200
  average time/residue: 0.1080
  time to fit residues: 33.2255
Evaluate side-chains
  198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 147
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  557 HIS
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  847 HIS
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  273 GLU
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  297 PHE
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 146 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 137 optimal weight:    0.9990
   chunk 142 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 GLN
C 280 HIS
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 GLN
D 301 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.137735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.115213 restraints weight = 37677.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.115957 restraints weight = 45258.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.116458 restraints weight = 39362.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.116951 restraints weight = 26215.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.117476 restraints weight = 22652.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14648  Z= 0.163
  Angle     :  0.644  15.604  20011  Z= 0.321
  Chirality :  0.042   0.206   2244
  Planarity :  0.004   0.048   2362
  Dihedral  :  7.917  83.336   2349
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.03 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.21), residues: 1610
  helix:  1.51 (0.21), residues: 583
  sheet: -1.85 (0.32), residues: 255
  loop : -2.16 (0.22), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 824 
 TYR   0.021   0.001   TYR C 548 
 PHE   0.017   0.001   PHE A 571 
 TRP   0.022   0.001   TRP D 257 
 HIS   0.004   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 (14639)
  covalent geometry    : angle       0.64357 /  0.32 (20007)
  SS BOND              : bond        0.00482 /  0.23 (    2)
  SS BOND              : angle       1.27999 /  0.97 (    4)
  hydrogen bonds       : bond        0.04010 /  2.60 (  563)
  hydrogen bonds       : angle       4.54500 /  3.10 ( 1592)
  metal coordination   : bond        0.00329 /  0.17 (    5)
  Misc. bond           : bond        0.00031 /  0.01 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 146
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.5222 (tp)
REVERT: A  266 THR cc_start: 0.5680 (OUTLIER) cc_final: 0.5148 (p)
REVERT: A  369 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7536 (mtt)
REVERT: A  525 MET cc_start: 0.5379 (tmm) cc_final: 0.5174 (tmm)
REVERT: A  711 LEU cc_start: 0.6213 (mt) cc_final: 0.5884 (mt)
REVERT: A  760 MET cc_start: 0.4975 (ppp) cc_final: 0.4234 (ppp)
REVERT: B  420 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.7247 (t-90)
REVERT: C  434 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9273 (mp)
REVERT: C  457 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7842 (pt0)
REVERT: C  611 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8868 (mp)
REVERT: D  277 ASP cc_start: 0.8353 (p0) cc_final: 0.8135 (p0)
REVERT: D  320 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7238 (mtm-85)
REVERT: D  338 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8555 (tp40)
  outliers start: 59
  outliers final: 47
  residues processed: 193
  average time/residue: 0.1083
  time to fit residues: 32.1822
Evaluate side-chains
  197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 143
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  557 HIS
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  429 GLN
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  847 HIS
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  273 GLU
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  288 GLN
Chi-restraints excluded: chain D residue  301 GLN
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 123 optimal weight:    0.0040
   chunk 30 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   chunk 158 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 155 optimal weight:    7.9990
   overall best weight:    1.5598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 GLN
C 495 ASN
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 GLN
D 301 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.138636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.114037 restraints weight = 37240.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.114998 restraints weight = 34918.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.115190 restraints weight = 30847.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.115658 restraints weight = 19608.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.115986 restraints weight = 17483.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14648  Z= 0.127
  Angle     :  0.620   9.997  20011  Z= 0.312
  Chirality :  0.042   0.226   2244
  Planarity :  0.004   0.049   2362
  Dihedral  :  7.885  84.832   2349
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.37 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.22), residues: 1610
  helix:  1.59 (0.21), residues: 583
  sheet: -1.82 (0.31), residues: 261
  loop : -2.10 (0.23), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 824 
 TYR   0.023   0.001   TYR C 548 
 PHE   0.019   0.001   PHE D 297 
 TRP   0.017   0.001   TRP D 257 
 HIS   0.004   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 (14639)
  covalent geometry    : angle       0.61961 /  0.31 (20007)
  SS BOND              : bond        0.00367 /  0.18 (    2)
  SS BOND              : angle       1.14649 /  0.83 (    4)
  hydrogen bonds       : bond        0.03868 /  2.51 (  563)
  hydrogen bonds       : angle       4.47441 /  3.06 ( 1592)
  metal coordination   : bond        0.00268 /  0.14 (    5)
  Misc. bond           : bond        0.00028 /  0.01 (    2)

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

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

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3220 Ramachandran restraints generated.
    1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 153
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5201 (tp)
REVERT: A  266 THR cc_start: 0.5653 (OUTLIER) cc_final: 0.5145 (p)
REVERT: A  369 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7595 (mtt)
REVERT: A  525 MET cc_start: 0.5296 (tmm) cc_final: 0.5087 (tmm)
REVERT: A  711 LEU cc_start: 0.6099 (mt) cc_final: 0.5713 (mt)
REVERT: A  760 MET cc_start: 0.4850 (ppp) cc_final: 0.4132 (ppp)
REVERT: A  772 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.6913 (m-30)
REVERT: B  420 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7343 (t-90)
REVERT: C  434 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9285 (mp)
REVERT: C  457 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7830 (pt0)
REVERT: C  611 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8845 (mp)
REVERT: D  320 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7638 (mtm-85)
REVERT: D  397 LYS cc_start: 0.6928 (ptpt) cc_final: 0.6560 (ptpp)
  outliers start: 57
  outliers final: 46
  residues processed: 195
  average time/residue: 0.1126
  time to fit residues: 33.5156
Evaluate side-chains
  199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 145
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  557 HIS
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  873 TRP
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  916 ILE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  429 GLN
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain C residue  294 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  434 LEU
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 GLN
Chi-restraints excluded: chain C residue  586 LEU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  834 LEU
Chi-restraints excluded: chain C residue  847 HIS
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  273 GLU
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  288 GLN
Chi-restraints excluded: chain D residue  297 PHE
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  317 VAL
Chi-restraints excluded: chain D residue  335 SER
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  363 VAL
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  428 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 138 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 66 optimal weight:   20.0000
   chunk 79 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 619 GLN
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 GLN
** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.137061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.114522 restraints weight = 37626.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.114150 restraints weight = 52308.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.115025 restraints weight = 46041.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.115226 restraints weight = 30127.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.116770 restraints weight = 24987.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14648  Z= 0.188
  Angle     :  0.669  15.867  20011  Z= 0.336
  Chirality :  0.043   0.213   2244
  Planarity :  0.004   0.049   2362
  Dihedral  :  7.977  82.836   2349
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.43 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.22), residues: 1610
  helix:  1.49 (0.21), residues: 583
  sheet: -1.80 (0.32), residues: 254
  loop : -2.18 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 824 
 TYR   0.017   0.002   TYR C 548 
 PHE   0.021   0.002   PHE D 254 
 TRP   0.023   0.001   TRP D 257 
 HIS   0.004   0.001   HIS D 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.19 (14639)
  covalent geometry    : angle       0.66893 /  0.34 (20007)
  SS BOND              : bond        0.00512 /  0.25 (    2)
  SS BOND              : angle       1.34491 /  1.03 (    4)
  hydrogen bonds       : bond        0.04128 /  2.70 (  563)
  hydrogen bonds       : angle       4.64995 /  3.18 ( 1592)
  metal coordination   : bond        0.00412 /  0.21 (    5)
  Misc. bond           : bond        0.00039 /  0.02 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2037.59 seconds
wall clock time: 36 minutes 28.11 seconds (2188.11 seconds total)