Starting phenix.real_space_refine
on Wed Feb  4 16:01:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8n_27252/02_2026/8d8n_27252.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8n_27252/02_2026/8d8n_27252.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8n_27252/02_2026/8d8n_27252.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8n_27252/02_2026/8d8n_27252.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d8n_27252/02_2026/8d8n_27252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8n_27252/02_2026/8d8n_27252.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.034
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      4      6.06       5
     P      56      5.49       5
     S      33      5.16       5
     C    6943      2.51       5
     N    1978      2.21       5
     O    2261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11275
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 10082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1256, 10082
          Classifications: {'peptide': 1256}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 57, 'TRANS': 1198}
          Chain breaks: 5
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 3, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 42
    Chain: "C"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 734
          Classifications: {'RNA': 35}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 4, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 21, 'rna3p': 13}
    Chain: "D"
      Number of atoms: 455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 455
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 1, 'rna3p': 19}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    668  SG  CYS B  83      34.918  38.620  15.837  1.00144.18           S
  ATOM    939  SG  CYS B 116      34.715  35.721  17.170  1.00147.58           S
  ATOM   3436  SG  CYS B 486      27.334  55.044  47.908  1.00128.06           S
  ATOM   3504  SG  CYS B 496      24.506  55.520  44.527  1.00118.68           S
  ATOM   3518  SG  CYS B 498      27.634  56.725  45.105  1.00111.43           S
  ATOM   5546  SG  CYS B 750      20.418  60.286  76.922  1.00144.62           S
  ATOM   7491  SG  CYS B1018      22.015  49.825 113.127  1.00164.52           S
  ATOM   7738  SG  CYS B1406      19.065  50.188 111.390  1.00169.95           S
  ATOM   7789  SG  CYS B1414      21.102  52.908 112.245  1.00150.23           S
  ATOM   7806  SG  CYS B1417      23.491  51.123 110.375  1.00144.38           S

  Time building chain proxies: 2.40, per 1000 atoms: 0.21
  Number of scatterers: 11275
  At special positions: 0
  Unit cell: (78.324, 91.164, 159.216, 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      4     29.99
     S      33     16.00
     P      56     15.00
     O    2261      8.00
     N    1978      7.00
     C    6943      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 409.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1801 "
        pdb="ZN    ZN B1801 " - pdb=" SG  CYS B 116 "
        pdb="ZN    ZN B1801 " - pdb=" SG  CYS B  83 "
      pdb="  ZN B1802 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B 486 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B 498 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B 496 "
      pdb="  ZN B1803 "
        pdb="ZN    ZN B1803 " - pdb=" SG  CYS B 750 "
      pdb="  ZN B1804 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B1018 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B1417 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B1406 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B1414 "
      Number of angles added : 6


  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2296

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 16 sheets defined
      30.8% alpha, 19.2% beta
      8 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 20 through 25
    Processing helix  chain 'B' and resid 27 through 31
    Processing helix  chain 'B' and resid 54 through 73
      removed outlier: 3.753A  pdb=" N   VAL B  58 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASN B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 129
      removed outlier: 3.768A  pdb=" N   ILE B 126 " --> pdb=" O   CYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 168
      removed outlier: 3.838A  pdb=" N   ILE B 167 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 210
      No H-bonds generated for 'chain 'B' and resid 208 through 210'
    Processing helix  chain 'B' and resid 211 through 219
      removed outlier: 3.894A  pdb=" N   LEU B 215 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 282
      removed outlier: 4.130A  pdb=" N   ARG B 269 " --> pdb=" O   ASN B 265 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS B 270 " --> pdb=" O   ASP B 266 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA B 278 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE B 279 " --> pdb=" O   ILE B 275 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASN B 282 " --> pdb=" O   ALA B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 4.169A  pdb=" N   ILE B 290 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 309
    Processing helix  chain 'B' and resid 334 through 345
      removed outlier: 4.144A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 370
    Processing helix  chain 'B' and resid 466 through 483
    Processing helix  chain 'B' and resid 498 through 505
    Processing helix  chain 'B' and resid 564 through 575
    Processing helix  chain 'B' and resid 589 through 593
      removed outlier: 3.743A  pdb=" N   THR B 592 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY B 593 " --> pdb=" O   ASP B 590 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 589 through 593'
    Processing helix  chain 'B' and resid 612 through 619
      removed outlier: 3.599A  pdb=" N   GLU B 619 " --> pdb=" O   GLU B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 623
      removed outlier: 3.616A  pdb=" N   ARG B 623 " --> pdb=" O   ARG B 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 620 through 623'
    Processing helix  chain 'B' and resid 627 through 632
      removed outlier: 4.126A  pdb=" N   GLU B 631 " --> pdb=" O   LYS B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 637
      removed outlier: 3.811A  pdb=" N   LEU B 637 " --> pdb=" O   GLU B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 659
    Processing helix  chain 'B' and resid 660 through 662
      No H-bonds generated for 'chain 'B' and resid 660 through 662'
    Processing helix  chain 'B' and resid 681 through 686
      removed outlier: 3.940A  pdb=" N   ALA B 685 " --> pdb=" O   ASP B 681 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B 686 " --> pdb=" O   THR B 682 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 681 through 686'
    Processing helix  chain 'B' and resid 718 through 735
      removed outlier: 3.584A  pdb=" N   HIS B 722 " --> pdb=" O   LYS B 718 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 753
      removed outlier: 3.759A  pdb=" N   ILE B 751 " --> pdb=" O   CYS B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 827 through 843
      removed outlier: 3.516A  pdb=" N   LEU B 831 " --> pdb=" O   GLY B 827 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 868 through 877
    Processing helix  chain 'B' and resid 910 through 914
      removed outlier: 3.654A  pdb=" N   GLN B 913 " --> pdb=" O   SER B 910 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 976 through 980
      removed outlier: 3.967A  pdb=" N   GLY B 979 " --> pdb=" O   LYS B 976 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASN B 980 " --> pdb=" O   LEU B 977 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 976 through 980'
    Processing helix  chain 'B' and resid 999 through 1016
      removed outlier: 4.057A  pdb=" N   LEU B1003 " --> pdb=" O   PRO B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1394 through 1399
      removed outlier: 3.591A  pdb=" N   LYS B1398 " --> pdb=" O   THR B1394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1400 through 1404
    Processing helix  chain 'B' and resid 1414 through 1421
    Processing helix  chain 'B' and resid 1463 through 1468
      removed outlier: 4.242A  pdb=" N   SER B1467 " --> pdb=" O   ARG B1463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1489 through 1492
    Processing helix  chain 'B' and resid 1493 through 1501
      removed outlier: 3.694A  pdb=" N   GLU B1499 " --> pdb=" O   LEU B1495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1528 through 1540
      removed outlier: 4.090A  pdb=" N   LEU B1532 " --> pdb=" O   ARG B1528 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY B1533 " --> pdb=" O   GLU B1529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1586 through 1603
      removed outlier: 3.672A  pdb=" N   GLY B1603 " --> pdb=" O   ILE B1599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1619 through 1629
      removed outlier: 3.674A  pdb=" N   LEU B1629 " --> pdb=" O   LEU B1625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1673 through 1682
    Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3
      removed outlier: 5.127A  pdb=" N   ARG B 203 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   ASN B 150 " --> pdb=" O   ARG B 203 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   THR B 205 " --> pdb=" O   PHE B 148 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   PHE B 148 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   SER B  51 " --> pdb=" O   LEU B 153 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   ARG B  14 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   TRP B  39 " --> pdb=" O   ARG B  14 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL B  16 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   TRP B  41 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   TRP B 190 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 9.514A  pdb=" N   GLU B  17 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 13.476A  pdb=" N   ARG B 188 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP B 185 " --> pdb=" O   ARG B 175 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ARG B 175 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3
      removed outlier: 4.015A  pdb=" N   VAL B   5 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 77
    Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 329
    Processing sheet with id=AA5, first strand: chain 'B' and resid 507 through 508
    Processing sheet with id=AA6, first strand: chain 'B' and resid 507 through 508
      removed outlier: 4.086A  pdb=" N   VAL B 414 " --> pdb=" O   LYS B 603 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 603 " --> pdb=" O   VAL B 414 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ARG B 416 " --> pdb=" O   ASP B 601 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ASP B 601 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   LYS B 418 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   LEU B 599 " --> pdb=" O   LYS B 418 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 528
      removed outlier: 3.896A  pdb=" N   ALA B 527 " --> pdb=" O   SER B 539 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   SER B 539 " --> pdb=" O   ALA B 527 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 698 through 699
      removed outlier: 6.247A  pdb=" N   PHE B 715 " --> pdb=" O   LEU B 769 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU B 769 " --> pdb=" O   PHE B 715 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 699
      removed outlier: 6.247A  pdb=" N   PHE B 715 " --> pdb=" O   LEU B 769 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU B 769 " --> pdb=" O   PHE B 715 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   GLN B 668 " --> pdb=" O   ILE B 863 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   ILE B 863 " --> pdb=" O   GLN B 668 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   THR B 670 " --> pdb=" O   ILE B 861 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   ILE B 861 " --> pdb=" O   THR B 670 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLU B 672 " --> pdb=" O   ALA B 859 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 782 through 785
    Processing sheet with id=AB2, first strand: chain 'B' and resid 920 through 921
    Processing sheet with id=AB3, first strand: chain 'B' and resid 924 through 927
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1429 through 1430
      removed outlier: 3.604A  pdb=" N   ASN B1526 " --> pdb=" O   LEU B 950 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU B 950 " --> pdb=" O   ASN B1526 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER B1566 " --> pdb=" O   ASN B 955 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   LYS B 957 " --> pdb=" O   ILE B1564 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   ILE B1564 " --> pdb=" O   LYS B 957 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   GLU B 959 " --> pdb=" O   ILE B1562 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   ILE B1562 " --> pdb=" O   GLU B 959 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1435 through 1436
      removed outlier: 3.604A  pdb=" N   ASN B1526 " --> pdb=" O   LEU B 950 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU B 950 " --> pdb=" O   ASN B1526 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER B1566 " --> pdb=" O   ASN B 955 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   LYS B 957 " --> pdb=" O   ILE B1564 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   ILE B1564 " --> pdb=" O   LYS B 957 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   GLU B 959 " --> pdb=" O   ILE B1562 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   ILE B1562 " --> pdb=" O   GLU B 959 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B1569 " --> pdb=" O   LYS B1580 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS B1580 " --> pdb=" O   THR B1569 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 985 through 986
      removed outlier: 6.698A  pdb=" N   LYS B 985 " --> pdb=" O   THR B1508 " (cutoff:3.500A)
      removed outlier: 8.953A  pdb=" N   GLU B1510 " --> pdb=" O   LYS B 985 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1029 through 1030
      removed outlier: 3.610A  pdb=" N   LYS B1389 " --> pdb=" O   TRP B1030 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    894 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      32 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2829
        1.33 -     1.45: 2504
        1.45 -     1.57: 6148
        1.57 -     1.69: 111
        1.69 -     1.81: 45
  Bond restraints: 11637
  Sorted by residual:
  bond pdb=" CA  TYR B 197 "
       pdb=" CB  TYR B 197 "
    ideal  model  delta    sigma   weight residual
    1.531  1.457  0.074 3.12e-02 1.03e+03 5.56e+00
  bond pdb=" CA  PHE B 423 "
       pdb=" CB  PHE B 423 "
    ideal  model  delta    sigma   weight residual
    1.534  1.500  0.035 1.60e-02 3.91e+03 4.75e+00
  bond pdb=" CB  TRP B 820 "
       pdb=" CG  TRP B 820 "
    ideal  model  delta    sigma   weight residual
    1.498  1.438  0.060 3.10e-02 1.04e+03 3.77e+00
  bond pdb=" C   GLY B 807 "
       pdb=" N   SER B 808 "
    ideal  model  delta    sigma   weight residual
    1.327  1.300  0.026 1.71e-02 3.42e+03 2.36e+00
  bond pdb=" N1    C C  31 "
       pdb=" C2    C C  31 "
    ideal  model  delta    sigma   weight residual
    1.397  1.367  0.030 2.00e-02 2.50e+03 2.31e+00
  ... (remaining 11632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 15466
        2.07 -     4.14: 428
        4.14 -     6.21: 42
        6.21 -     8.28: 12
        8.28 -    10.35: 5
  Bond angle restraints: 15953
  Sorted by residual:
  angle pdb=" N   PRO B 911 "
        pdb=" CA  PRO B 911 "
        pdb=" CB  PRO B 911 "
      ideal   model   delta    sigma   weight residual
     103.25  112.54   -9.29 1.05e+00 9.07e-01 7.82e+01
  angle pdb=" N   PRO B 898 "
        pdb=" CA  PRO B 898 "
        pdb=" CB  PRO B 898 "
      ideal   model   delta    sigma   weight residual
     103.25  111.26   -8.01 1.05e+00 9.07e-01 5.81e+01
  angle pdb=" N   PRO B 906 "
        pdb=" CA  PRO B 906 "
        pdb=" CB  PRO B 906 "
      ideal   model   delta    sigma   weight residual
     103.25  109.92   -6.67 1.05e+00 9.07e-01 4.04e+01
  angle pdb=" C   SER B 910 "
        pdb=" N   PRO B 911 "
        pdb=" CA  PRO B 911 "
      ideal   model   delta    sigma   weight residual
     119.84  127.28   -7.44 1.25e+00 6.40e-01 3.54e+01
  angle pdb=" N   ILE B 447 "
        pdb=" CA  ILE B 447 "
        pdb=" C   ILE B 447 "
      ideal   model   delta    sigma   weight residual
     111.91  107.64    4.27 8.90e-01 1.26e+00 2.30e+01
  ... (remaining 15948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.65: 6767
       35.65 -    71.29: 241
       71.29 -   106.94: 34
      106.94 -   142.59: 1
      142.59 -   178.23: 3
  Dihedral angle restraints: 7046
    sinusoidal: 3461
      harmonic: 3585
  Sorted by residual:
  dihedral pdb=" O4'   C C  22 "
           pdb=" C1'   C C  22 "
           pdb=" N1    C C  22 "
           pdb=" C2    C C  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.09  146.91     1      1.50e+01 4.44e-03 7.84e+01
  dihedral pdb=" CA  GLY B1439 "
           pdb=" C   GLY B1439 "
           pdb=" N   PRO B1440 "
           pdb=" CA  PRO B1440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.09  -40.91     0      5.00e+00 4.00e-02 6.70e+01
  dihedral pdb=" O4'   U C  27 "
           pdb=" C1'   U C  27 "
           pdb=" N1    U C  27 "
           pdb=" C2    U C  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.77  178.23     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 7043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1451
       0.061 -    0.121: 266
       0.121 -    0.182: 22
       0.182 -    0.243: 1
       0.243 -    0.303: 3
  Chirality restraints: 1743
  Sorted by residual:
  chirality pdb=" CA  PRO B 911 "
            pdb=" N   PRO B 911 "
            pdb=" C   PRO B 911 "
            pdb=" CB  PRO B 911 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  PRO B 906 "
            pdb=" N   PRO B 906 "
            pdb=" C   PRO B 906 "
            pdb=" CB  PRO B 906 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" C1'   A C  13 "
            pdb=" O4'   A C  13 "
            pdb=" C2'   A C  13 "
            pdb=" N9    A C  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.20    0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1740 not shown)

  Planarity restraints: 1855
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  99 "   -0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   PHE B  99 "    0.060 2.00e-02 2.50e+03
        pdb=" O   PHE B  99 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 100 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  36 "    0.011 2.00e-02 2.50e+03   1.51e-02 6.80e+00
        pdb=" N9    G D  36 "   -0.005 2.00e-02 2.50e+03
        pdb=" C8    G D  36 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G D  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G D  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G D  36 "   -0.027 2.00e-02 2.50e+03
        pdb=" O6    G D  36 "    0.028 2.00e-02 2.50e+03
        pdb=" N1    G D  36 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    G D  36 "   -0.027 2.00e-02 2.50e+03
        pdb=" N2    G D  36 "    0.015 2.00e-02 2.50e+03
        pdb=" N3    G D  36 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G D  36 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  13 "   -0.032 2.00e-02 2.50e+03   1.49e-02 6.08e+00
        pdb=" N9    A C  13 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    A C  13 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A C  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A C  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A C  13 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A C  13 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    A C  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A C  13 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A C  13 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A C  13 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1852 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 89
        2.44 -     3.06: 7882
        3.06 -     3.67: 16286
        3.67 -     4.29: 22723
        4.29 -     4.90: 36637
  Nonbonded interactions: 83617
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 745 "
            pdb="ZN    ZN B1803 "
     model   vdw
     1.828 2.230
  nonbonded pdb=" O   ILE B 115 "
            pdb="ZN    ZN B1801 "
     model   vdw
     1.944 2.230
  nonbonded pdb=" N4    C C  29 "
            pdb=" N6    A D  37 "
     model   vdw
     2.078 2.560
  nonbonded pdb=" O2'   U C  16 "
            pdb=" O4'   A C  17 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" NE  ARG B 101 "
            pdb=" O5'   U C  21 "
     model   vdw
     2.116 3.120
  ... (remaining 83612 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.580
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.141  11647  Z= 0.366
  Angle     :  0.986  55.277  15959  Z= 0.491
  Chirality :  0.047   0.303   1743
  Planarity :  0.005   0.058   1855
  Dihedral  : 18.210 178.235   4750
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 11.17 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  8.05 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.25 %

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: -4.01 (0.19), residues: 1244
  helix: -1.90 (0.23), residues: 315
  sheet: -2.52 (0.32), residues: 180
  loop : -3.20 (0.19), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 140 
 TYR   0.018   0.002   TYR B 616 
 PHE   0.021   0.002   PHE B  52 
 TRP   0.010   0.002   TRP B  21 
 HIS   0.008   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 (11637)
  covalent geometry    : angle       0.84145 (15953)
  hydrogen bonds       : bond        0.20375 (  318)
  hydrogen bonds       : angle       8.40446 (  926)
  metal coordination   : bond        0.06410 (   10)
  metal coordination   : angle      26.48146 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  164 LEU cc_start: 0.8689 (tp) cc_final: 0.8413 (tp)
REVERT: B  166 ASP cc_start: 0.8419 (m-30) cc_final: 0.8144 (t0)
REVERT: B  172 ILE cc_start: 0.8441 (mt) cc_final: 0.8128 (tt)
REVERT: B  178 PHE cc_start: 0.7726 (t80) cc_final: 0.7388 (t80)
REVERT: B  213 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7880 (pttp)
REVERT: B  343 GLN cc_start: 0.8875 (tp40) cc_final: 0.8299 (mp10)
REVERT: B  362 TYR cc_start: 0.7946 (t80) cc_final: 0.7649 (t80)
REVERT: B  562 LYS cc_start: 0.8940 (tppt) cc_final: 0.8707 (tttp)
REVERT: B  618 LYS cc_start: 0.9101 (tppt) cc_final: 0.8652 (ttpt)
REVERT: B  627 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8853 (tptt)
REVERT: B  652 CYS cc_start: 0.8255 (m) cc_final: 0.7580 (t)
REVERT: B 1028 LEU cc_start: 0.7714 (pt) cc_final: 0.7509 (pp)
REVERT: B 1500 THR cc_start: 0.9426 (t) cc_final: 0.9130 (p)
REVERT: B 1578 LYS cc_start: 0.6302 (mmtt) cc_final: 0.5944 (mmtt)
REVERT: B 1600 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8391 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 167
  average time/residue: 0.1000
  time to fit residues: 23.8576
Evaluate side-chains
  85 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue 1629 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0270
   chunk 55 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
B  34 GLN
B 155 HIS
B 281 GLN
B 301 HIS
B 691 ASN
B 771 ASN
B 980 ASN
B1418 HIS
B1483 HIS
** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1544 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.118230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.087953 restraints weight = 20537.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.091436 restraints weight = 10213.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.093762 restraints weight = 6802.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.095243 restraints weight = 5339.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.096177 restraints weight = 4603.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11647  Z= 0.133
  Angle     :  0.623   9.264  15959  Z= 0.322
  Chirality :  0.043   0.241   1743
  Planarity :  0.005   0.048   1855
  Dihedral  : 18.312 178.101   2224
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.87 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.03 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.25 %

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: -2.36 (0.22), residues: 1244
  helix:  0.03 (0.28), residues: 336
  sheet: -1.52 (0.34), residues: 187
  loop : -2.48 (0.21), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 130 
 TYR   0.012   0.001   TYR B 558 
 PHE   0.016   0.001   PHE B1520 
 TRP   0.012   0.001   TRP B 585 
 HIS   0.007   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (11637)
  covalent geometry    : angle       0.61914 (15953)
  hydrogen bonds       : bond        0.06247 (  318)
  hydrogen bonds       : angle       5.29552 (  926)
  metal coordination   : bond        0.00532 (   10)
  metal coordination   : angle       3.84375 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  164 LEU cc_start: 0.7903 (tp) cc_final: 0.7618 (tp)
REVERT: B  166 ASP cc_start: 0.8377 (m-30) cc_final: 0.8017 (t0)
REVERT: B  178 PHE cc_start: 0.7649 (t80) cc_final: 0.7345 (t80)
REVERT: B  213 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7668 (pttp)
REVERT: B  343 GLN cc_start: 0.8728 (tp40) cc_final: 0.8373 (mp10)
REVERT: B  362 TYR cc_start: 0.8378 (t80) cc_final: 0.8063 (t80)
REVERT: B  608 ASP cc_start: 0.7089 (t0) cc_final: 0.6812 (t70)
REVERT: B  618 LYS cc_start: 0.9092 (tppt) cc_final: 0.8760 (ttpt)
REVERT: B  639 ASP cc_start: 0.7855 (p0) cc_final: 0.7578 (t70)
REVERT: B  652 CYS cc_start: 0.8062 (m) cc_final: 0.7432 (t)
REVERT: B  874 MET cc_start: 0.5195 (mtp) cc_final: 0.4977 (mtp)
REVERT: B 1028 LEU cc_start: 0.8251 (pt) cc_final: 0.7745 (pp)
REVERT: B 1571 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7964 (mttt)
  outliers start: 20
  outliers final: 10
  residues processed: 113
  average time/residue: 0.0846
  time to fit residues: 14.1354
Evaluate side-chains
  78 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1453 SER
Chi-restraints excluded: chain B residue 1467 SER
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1589 GLU
Chi-restraints excluded: chain B residue 1629 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 63 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
B 104 HIS
B 112 ASN
B 150 ASN
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 722 HIS
B 784 HIS
B 917 ASN
** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1575 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.078800 restraints weight = 20847.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.081969 restraints weight = 10757.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.084083 restraints weight = 7386.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.085423 restraints weight = 5902.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.086202 restraints weight = 5152.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11647  Z= 0.234
  Angle     :  0.668   9.210  15959  Z= 0.344
  Chirality :  0.044   0.226   1743
  Planarity :  0.005   0.053   1855
  Dihedral  : 18.107 175.569   2223
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.56 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 13.51 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.91 (0.23), residues: 1244
  helix:  0.50 (0.29), residues: 321
  sheet: -1.43 (0.36), residues: 188
  loop : -2.14 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B1498 
 TYR   0.020   0.002   TYR B 558 
 PHE   0.022   0.002   PHE B1520 
 TRP   0.019   0.002   TRP B1030 
 HIS   0.005   0.001   HIS B 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (11637)
  covalent geometry    : angle       0.66341 (15953)
  hydrogen bonds       : bond        0.06957 (  318)
  hydrogen bonds       : angle       5.12360 (  926)
  metal coordination   : bond        0.00784 (   10)
  metal coordination   : angle       3.87257 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 ASP cc_start: 0.8372 (m-30) cc_final: 0.8018 (t0)
REVERT: B  178 PHE cc_start: 0.7977 (t80) cc_final: 0.7494 (t80)
REVERT: B  343 GLN cc_start: 0.8721 (tp40) cc_final: 0.8162 (mp10)
REVERT: B  458 ASP cc_start: 0.8361 (t0) cc_final: 0.8157 (t0)
REVERT: B  652 CYS cc_start: 0.8163 (m) cc_final: 0.7812 (t)
REVERT: B  742 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5696 (t-170)
REVERT: B 1028 LEU cc_start: 0.8483 (pt) cc_final: 0.8263 (pp)
REVERT: B 1401 LYS cc_start: 0.8276 (tptt) cc_final: 0.7882 (mtpp)
  outliers start: 34
  outliers final: 23
  residues processed: 99
  average time/residue: 0.0894
  time to fit residues: 13.4414
Evaluate side-chains
  80 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  627 LYS
Chi-restraints excluded: chain B residue  742 HIS
Chi-restraints excluded: chain B residue  751 ILE
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1393 LYS
Chi-restraints excluded: chain B residue 1395 LEU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1629 LEU
Chi-restraints excluded: chain B residue 1647 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 105 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 122 optimal weight:    0.7980
   chunk 116 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 561 HIS
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 876 ASN
** B1485 ASN ** 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 = 0.3575 r_free = 0.3575 target = 0.111808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.080529 restraints weight = 20618.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.083828 restraints weight = 10616.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.086035 restraints weight = 7270.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.087377 restraints weight = 5794.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.088302 restraints weight = 5058.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11647  Z= 0.135
  Angle     :  0.571   9.465  15959  Z= 0.292
  Chirality :  0.041   0.223   1743
  Planarity :  0.004   0.050   1855
  Dihedral  : 17.998 177.259   2223
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.55 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.36 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.56 (0.23), residues: 1244
  helix:  0.98 (0.30), residues: 325
  sheet: -1.16 (0.36), residues: 189
  loop : -2.06 (0.21), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1528 
 TYR   0.009   0.001   TYR B 558 
 PHE   0.018   0.001   PHE B1520 
 TRP   0.007   0.001   TRP B 190 
 HIS   0.004   0.001   HIS B 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11637)
  covalent geometry    : angle       0.56956 (15953)
  hydrogen bonds       : bond        0.05935 (  318)
  hydrogen bonds       : angle       4.64274 (  926)
  metal coordination   : bond        0.00325 (   10)
  metal coordination   : angle       2.17822 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 TRP cc_start: 0.7715 (t-100) cc_final: 0.7298 (t-100)
REVERT: B  166 ASP cc_start: 0.8354 (m-30) cc_final: 0.7984 (t0)
REVERT: B  178 PHE cc_start: 0.7849 (t80) cc_final: 0.7415 (t80)
REVERT: B  343 GLN cc_start: 0.8688 (tp40) cc_final: 0.8198 (mp10)
REVERT: B  618 LYS cc_start: 0.9005 (tppt) cc_final: 0.8577 (ttpt)
REVERT: B  639 ASP cc_start: 0.8006 (p0) cc_final: 0.7414 (t70)
REVERT: B  652 CYS cc_start: 0.8085 (m) cc_final: 0.7722 (t)
REVERT: B  972 GLU cc_start: 0.8564 (tp30) cc_final: 0.8278 (tp30)
REVERT: B 1028 LEU cc_start: 0.8481 (pt) cc_final: 0.8042 (pp)
REVERT: B 1401 LYS cc_start: 0.8161 (tptt) cc_final: 0.7917 (mtpp)
REVERT: B 1422 THR cc_start: 0.8248 (t) cc_final: 0.8018 (m)
REVERT: B 1607 ILE cc_start: 0.1817 (OUTLIER) cc_final: 0.1586 (mt)
  outliers start: 30
  outliers final: 19
  residues processed: 99
  average time/residue: 0.0863
  time to fit residues: 13.1881
Evaluate side-chains
  83 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  920 ILE
Chi-restraints excluded: chain B residue  946 THR
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1024 GLU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1607 ILE
Chi-restraints excluded: chain B residue 1647 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 126 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
B 150 ASN
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 991 ASN
** B1485 ASN ** 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 = 0.3540 r_free = 0.3540 target = 0.109414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.078463 restraints weight = 20591.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.081672 restraints weight = 10672.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.083769 restraints weight = 7336.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.085107 restraints weight = 5877.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.085954 restraints weight = 5136.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11647  Z= 0.182
  Angle     :  0.600   9.456  15959  Z= 0.307
  Chirality :  0.042   0.217   1743
  Planarity :  0.005   0.051   1855
  Dihedral  : 17.939 176.789   2221
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.56 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.91 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.42 (0.23), residues: 1244
  helix:  1.19 (0.30), residues: 316
  sheet: -1.20 (0.35), residues: 189
  loop : -1.93 (0.22), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1498 
 TYR   0.012   0.001   TYR B 558 
 PHE   0.020   0.001   PHE B1520 
 TRP   0.008   0.001   TRP B1616 
 HIS   0.005   0.001   HIS B 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (11637)
  covalent geometry    : angle       0.59726 (15953)
  hydrogen bonds       : bond        0.06270 (  318)
  hydrogen bonds       : angle       4.63283 (  926)
  metal coordination   : bond        0.00546 (   10)
  metal coordination   : angle       2.77636 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 62
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 TRP cc_start: 0.7720 (t-100) cc_final: 0.7255 (t-100)
REVERT: B  166 ASP cc_start: 0.8336 (m-30) cc_final: 0.7931 (t0)
REVERT: B  178 PHE cc_start: 0.7845 (t80) cc_final: 0.7381 (t80)
REVERT: B  343 GLN cc_start: 0.8732 (tp40) cc_final: 0.8366 (tm-30)
REVERT: B  458 ASP cc_start: 0.8398 (t0) cc_final: 0.8180 (t0)
REVERT: B  618 LYS cc_start: 0.9004 (tppt) cc_final: 0.8570 (ttpt)
REVERT: B  652 CYS cc_start: 0.8083 (m) cc_final: 0.7799 (t)
REVERT: B  742 HIS cc_start: 0.5710 (OUTLIER) cc_final: 0.5487 (t-170)
REVERT: B  864 ASP cc_start: 0.8234 (t70) cc_final: 0.7314 (p0)
REVERT: B  972 GLU cc_start: 0.8562 (tp30) cc_final: 0.8230 (tp30)
REVERT: B 1028 LEU cc_start: 0.8499 (pt) cc_final: 0.8164 (pp)
REVERT: B 1538 SER cc_start: 0.9425 (t) cc_final: 0.9020 (p)
  outliers start: 37
  outliers final: 27
  residues processed: 94
  average time/residue: 0.0820
  time to fit residues: 12.0464
Evaluate side-chains
  87 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 59
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  230 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  610 ASN
Chi-restraints excluded: chain B residue  632 MET
Chi-restraints excluded: chain B residue  742 HIS
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  946 THR
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1393 LYS
Chi-restraints excluded: chain B residue 1395 LEU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1489 ILE
Chi-restraints excluded: chain B residue 1495 LEU
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1572 ILE
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1647 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0870
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 125 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    2.2166

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

Flipped N/Q/H residues before XYZ refinement:
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN
B1483 HIS
** B1485 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 = 0.3506 r_free = 0.3506 target = 0.107135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.076189 restraints weight = 20699.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.079339 restraints weight = 10863.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.081426 restraints weight = 7525.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.082790 restraints weight = 6043.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.083612 restraints weight = 5265.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  11647  Z= 0.241
  Angle     :  0.658   9.348  15959  Z= 0.337
  Chirality :  0.044   0.215   1743
  Planarity :  0.005   0.054   1855
  Dihedral  : 17.996 178.626   2221
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.96 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 16.84 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.56 (0.23), residues: 1244
  helix:  0.99 (0.30), residues: 315
  sheet: -1.35 (0.35), residues: 186
  loop : -1.96 (0.21), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 818 
 TYR   0.017   0.002   TYR B 558 
 PHE   0.021   0.002   PHE B1520 
 TRP   0.013   0.001   TRP B1601 
 HIS   0.006   0.001   HIS B 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (11637)
  covalent geometry    : angle       0.65475 (15953)
  hydrogen bonds       : bond        0.06762 (  318)
  hydrogen bonds       : angle       4.80583 (  926)
  metal coordination   : bond        0.00819 (   10)
  metal coordination   : angle       3.17179 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 64
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: B   39 TRP cc_start: 0.7817 (t-100) cc_final: 0.7366 (t-100)
REVERT: B   67 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7419 (mt-10)
REVERT: B  139 GLU cc_start: 0.7208 (pp20) cc_final: 0.6926 (pp20)
REVERT: B  166 ASP cc_start: 0.8351 (m-30) cc_final: 0.7950 (t0)
REVERT: B  178 PHE cc_start: 0.8017 (t80) cc_final: 0.7474 (t80)
REVERT: B  343 GLN cc_start: 0.8742 (tp40) cc_final: 0.8370 (tm-30)
REVERT: B  608 ASP cc_start: 0.8266 (t0) cc_final: 0.8040 (t0)
REVERT: B  618 LYS cc_start: 0.9056 (tppt) cc_final: 0.8662 (ttpt)
REVERT: B  652 CYS cc_start: 0.8070 (m) cc_final: 0.7845 (t)
REVERT: B  688 GLU cc_start: 0.8325 (tp30) cc_final: 0.7546 (tm-30)
REVERT: B  742 HIS cc_start: 0.5752 (OUTLIER) cc_final: 0.5441 (t-170)
REVERT: B  972 GLU cc_start: 0.8521 (tp30) cc_final: 0.8181 (tp30)
REVERT: B 1538 SER cc_start: 0.9415 (t) cc_final: 0.9042 (p)
  outliers start: 39
  outliers final: 29
  residues processed: 99
  average time/residue: 0.0820
  time to fit residues: 12.5068
Evaluate side-chains
  87 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 57
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  230 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  570 VAL
Chi-restraints excluded: chain B residue  632 MET
Chi-restraints excluded: chain B residue  742 HIS
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  920 ILE
Chi-restraints excluded: chain B residue  946 THR
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1393 LYS
Chi-restraints excluded: chain B residue 1395 LEU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1489 ILE
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1572 ILE
Chi-restraints excluded: chain B residue 1582 VAL
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1647 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 123 optimal weight:    0.0170
   chunk 13 optimal weight:    4.9990
   chunk 125 optimal weight:    8.9990
   overall best weight:    1.3624

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

Flipped N/Q/H residues before XYZ refinement:
B 561 HIS
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.109047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.078003 restraints weight = 20582.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.081261 restraints weight = 10698.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.083397 restraints weight = 7380.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.084728 restraints weight = 5915.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.085601 restraints weight = 5171.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11647  Z= 0.162
  Angle     :  0.600   9.405  15959  Z= 0.306
  Chirality :  0.041   0.220   1743
  Planarity :  0.004   0.052   1855
  Dihedral  : 17.798 178.840   2217
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.67 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.41 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.40 (0.23), residues: 1244
  helix:  1.18 (0.30), residues: 320
  sheet: -1.27 (0.35), residues: 181
  loop : -1.90 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 733 
 TYR   0.011   0.001   TYR B 558 
 PHE   0.019   0.001   PHE B1520 
 TRP   0.006   0.001   TRP B 664 
 HIS   0.005   0.001   HIS B 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (11637)
  covalent geometry    : angle       0.59802 (15953)
  hydrogen bonds       : bond        0.06004 (  318)
  hydrogen bonds       : angle       4.52710 (  926)
  metal coordination   : bond        0.00412 (   10)
  metal coordination   : angle       2.48007 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 63
  time to evaluate  : 0.391 
Fit side-chains
REVERT: B   39 TRP cc_start: 0.7689 (t-100) cc_final: 0.7201 (t-100)
REVERT: B   67 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7360 (mt-10)
REVERT: B  139 GLU cc_start: 0.7220 (pp20) cc_final: 0.6977 (pp20)
REVERT: B  166 ASP cc_start: 0.8319 (m-30) cc_final: 0.7948 (t0)
REVERT: B  178 PHE cc_start: 0.7972 (t80) cc_final: 0.7470 (t80)
REVERT: B  232 ILE cc_start: 0.8891 (mt) cc_final: 0.8324 (tt)
REVERT: B  343 GLN cc_start: 0.8722 (tp40) cc_final: 0.8412 (tm-30)
REVERT: B  608 ASP cc_start: 0.8272 (t0) cc_final: 0.8067 (t0)
REVERT: B  652 CYS cc_start: 0.8077 (m) cc_final: 0.7846 (t)
REVERT: B  688 GLU cc_start: 0.8266 (tp30) cc_final: 0.7452 (tm-30)
REVERT: B  742 HIS cc_start: 0.5697 (OUTLIER) cc_final: 0.5345 (t-170)
REVERT: B  972 GLU cc_start: 0.8492 (tp30) cc_final: 0.8148 (tp30)
REVERT: B 1028 LEU cc_start: 0.8508 (pt) cc_final: 0.8285 (pp)
REVERT: B 1538 SER cc_start: 0.9435 (t) cc_final: 0.9036 (p)
REVERT: B 1672 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8012 (tt)
  outliers start: 34
  outliers final: 26
  residues processed: 94
  average time/residue: 0.0753
  time to fit residues: 10.9636
Evaluate side-chains
  90 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  230 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  742 HIS
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  920 ILE
Chi-restraints excluded: chain B residue  946 THR
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1393 LYS
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1520 PHE
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1572 ILE
Chi-restraints excluded: chain B residue 1582 VAL
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1647 VAL
Chi-restraints excluded: chain B residue 1672 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 127 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 108 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 129 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 112 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 561 HIS
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.109926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.077728 restraints weight = 19728.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.081185 restraints weight = 9918.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.083480 restraints weight = 6714.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.084937 restraints weight = 5322.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.085788 restraints weight = 4615.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11647  Z= 0.130
  Angle     :  0.579   9.410  15959  Z= 0.294
  Chirality :  0.040   0.220   1743
  Planarity :  0.004   0.050   1855
  Dihedral  : 17.674 179.857   2217
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.59 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.96 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.15 (0.24), residues: 1244
  helix:  1.45 (0.30), residues: 320
  sheet: -1.15 (0.35), residues: 181
  loop : -1.76 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 623 
 TYR   0.009   0.001   TYR B 803 
 PHE   0.017   0.001   PHE B1520 
 TRP   0.010   0.001   TRP B  39 
 HIS   0.004   0.001   HIS B 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11637)
  covalent geometry    : angle       0.57734 (15953)
  hydrogen bonds       : bond        0.05559 (  318)
  hydrogen bonds       : angle       4.38327 (  926)
  metal coordination   : bond        0.00279 (   10)
  metal coordination   : angle       2.49762 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 66
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: B   39 TRP cc_start: 0.7182 (t-100) cc_final: 0.6459 (t-100)
REVERT: B   67 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7297 (mt-10)
REVERT: B  139 GLU cc_start: 0.7199 (pp20) cc_final: 0.6936 (pp20)
REVERT: B  166 ASP cc_start: 0.8357 (m-30) cc_final: 0.7933 (t0)
REVERT: B  178 PHE cc_start: 0.8002 (t80) cc_final: 0.7364 (t80)
REVERT: B  232 ILE cc_start: 0.8753 (mt) cc_final: 0.8175 (tt)
REVERT: B  343 GLN cc_start: 0.8681 (tp40) cc_final: 0.8321 (tm-30)
REVERT: B  577 ASN cc_start: 0.8059 (m-40) cc_final: 0.7619 (t0)
REVERT: B  608 ASP cc_start: 0.8333 (t0) cc_final: 0.8110 (t0)
REVERT: B  618 LYS cc_start: 0.8978 (tppt) cc_final: 0.8487 (ttpt)
REVERT: B  639 ASP cc_start: 0.8031 (p0) cc_final: 0.7350 (t70)
REVERT: B  652 CYS cc_start: 0.8150 (m) cc_final: 0.7893 (t)
REVERT: B  688 GLU cc_start: 0.8221 (tp30) cc_final: 0.7121 (pp20)
REVERT: B  720 GLU cc_start: 0.8541 (mp0) cc_final: 0.8223 (mp0)
REVERT: B  972 GLU cc_start: 0.8473 (tp30) cc_final: 0.8115 (tp30)
REVERT: B 1028 LEU cc_start: 0.8413 (pt) cc_final: 0.8170 (pp)
REVERT: B 1538 SER cc_start: 0.9437 (t) cc_final: 0.8993 (p)
REVERT: B 1672 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7801 (tt)
  outliers start: 30
  outliers final: 24
  residues processed: 93
  average time/residue: 0.0850
  time to fit residues: 12.2921
Evaluate side-chains
  86 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  230 CYS
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  920 ILE
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1393 LYS
Chi-restraints excluded: chain B residue 1395 LEU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1489 ILE
Chi-restraints excluded: chain B residue 1520 PHE
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1572 ILE
Chi-restraints excluded: chain B residue 1582 VAL
Chi-restraints excluded: chain B residue 1647 VAL
Chi-restraints excluded: chain B residue 1672 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 47 optimal weight:    7.9990
   chunk 123 optimal weight:    0.4980
   chunk 129 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 121 optimal weight:    0.4980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 561 HIS
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN
** B1485 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 = 0.3535 r_free = 0.3535 target = 0.111846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.079370 restraints weight = 19737.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.082877 restraints weight = 9979.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.085217 restraints weight = 6775.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.086676 restraints weight = 5365.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.087552 restraints weight = 4663.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.5033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11647  Z= 0.109
  Angle     :  0.561   9.564  15959  Z= 0.284
  Chirality :  0.040   0.218   1743
  Planarity :  0.004   0.051   1855
  Dihedral  : 17.527 179.236   2217
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.55 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.43 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -0.98 (0.24), residues: 1244
  helix:  1.61 (0.31), residues: 321
  sheet: -0.95 (0.35), residues: 185
  loop : -1.69 (0.22), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1505 
 TYR   0.010   0.001   TYR B 803 
 PHE   0.016   0.001   PHE B1520 
 TRP   0.007   0.001   TRP B 585 
 HIS   0.003   0.001   HIS B1621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11637)
  covalent geometry    : angle       0.55848 (15953)
  hydrogen bonds       : bond        0.05213 (  318)
  hydrogen bonds       : angle       4.15078 (  926)
  metal coordination   : bond        0.00185 (   10)
  metal coordination   : angle       2.69912 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 0.324 
Fit side-chains
REVERT: B   39 TRP cc_start: 0.7191 (t-100) cc_final: 0.6686 (t-100)
REVERT: B   67 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7256 (mt-10)
REVERT: B  166 ASP cc_start: 0.8313 (m-30) cc_final: 0.7861 (t0)
REVERT: B  178 PHE cc_start: 0.7985 (t80) cc_final: 0.7348 (t80)
REVERT: B  232 ILE cc_start: 0.8754 (mt) cc_final: 0.8253 (tt)
REVERT: B  343 GLN cc_start: 0.8631 (tp40) cc_final: 0.8321 (tm-30)
REVERT: B  362 TYR cc_start: 0.8273 (t80) cc_final: 0.8059 (t80)
REVERT: B  577 ASN cc_start: 0.7986 (m-40) cc_final: 0.7567 (t0)
REVERT: B  608 ASP cc_start: 0.8275 (t0) cc_final: 0.7874 (t0)
REVERT: B  618 LYS cc_start: 0.8823 (tppt) cc_final: 0.8349 (ttpt)
REVERT: B  639 ASP cc_start: 0.7892 (p0) cc_final: 0.7247 (t70)
REVERT: B  688 GLU cc_start: 0.8173 (tp30) cc_final: 0.7004 (pp20)
REVERT: B  720 GLU cc_start: 0.8555 (mp0) cc_final: 0.8237 (mp0)
REVERT: B  742 HIS cc_start: 0.5715 (OUTLIER) cc_final: 0.5273 (t-170)
REVERT: B  972 GLU cc_start: 0.8433 (tp30) cc_final: 0.8094 (tp30)
REVERT: B 1028 LEU cc_start: 0.8508 (pt) cc_final: 0.8225 (pp)
REVERT: B 1538 SER cc_start: 0.9400 (t) cc_final: 0.8926 (p)
REVERT: B 1672 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7804 (tt)
  outliers start: 29
  outliers final: 25
  residues processed: 90
  average time/residue: 0.0820
  time to fit residues: 11.6332
Evaluate side-chains
  88 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  230 CYS
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  561 HIS
Chi-restraints excluded: chain B residue  632 MET
Chi-restraints excluded: chain B residue  742 HIS
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  920 ILE
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1395 LEU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1520 PHE
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1572 ILE
Chi-restraints excluded: chain B residue 1582 VAL
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1647 VAL
Chi-restraints excluded: chain B residue 1672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 119 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B 561 HIS
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.110524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.078009 restraints weight = 19917.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.081487 restraints weight = 9965.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.083797 restraints weight = 6733.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.085223 restraints weight = 5333.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.086115 restraints weight = 4637.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.5059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11647  Z= 0.142
  Angle     :  0.588   9.586  15959  Z= 0.298
  Chirality :  0.040   0.217   1743
  Planarity :  0.004   0.055   1855
  Dihedral  : 17.526 179.451   2217
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.43 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.52 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -0.96 (0.24), residues: 1244
  helix:  1.59 (0.30), residues: 321
  sheet: -0.95 (0.35), residues: 186
  loop : -1.66 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 623 
 TYR   0.013   0.001   TYR B 558 
 PHE   0.018   0.001   PHE B1520 
 TRP   0.006   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B1483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11637)
  covalent geometry    : angle       0.58589 (15953)
  hydrogen bonds       : bond        0.05405 (  318)
  hydrogen bonds       : angle       4.21744 (  926)
  metal coordination   : bond        0.00370 (   10)
  metal coordination   : angle       2.54057 (    6)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.303 
Fit side-chains
REVERT: B   39 TRP cc_start: 0.7297 (t-100) cc_final: 0.6653 (t-100)
REVERT: B   67 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7294 (mt-10)
REVERT: B  166 ASP cc_start: 0.8288 (m-30) cc_final: 0.7880 (t0)
REVERT: B  178 PHE cc_start: 0.8025 (t80) cc_final: 0.7425 (t80)
REVERT: B  232 ILE cc_start: 0.8772 (mt) cc_final: 0.8211 (tt)
REVERT: B  343 GLN cc_start: 0.8705 (tp40) cc_final: 0.8353 (tm-30)
REVERT: B  577 ASN cc_start: 0.8070 (m-40) cc_final: 0.7642 (t0)
REVERT: B  608 ASP cc_start: 0.8289 (t0) cc_final: 0.7905 (t0)
REVERT: B  618 LYS cc_start: 0.8895 (tppt) cc_final: 0.8423 (ttpt)
REVERT: B  639 ASP cc_start: 0.7924 (p0) cc_final: 0.7276 (t70)
REVERT: B  688 GLU cc_start: 0.8183 (tp30) cc_final: 0.7127 (pp20)
REVERT: B  720 GLU cc_start: 0.8544 (mp0) cc_final: 0.8210 (mp0)
REVERT: B  742 HIS cc_start: 0.5779 (OUTLIER) cc_final: 0.5357 (t-170)
REVERT: B  972 GLU cc_start: 0.8413 (tp30) cc_final: 0.8095 (tp30)
REVERT: B 1028 LEU cc_start: 0.8482 (pt) cc_final: 0.8234 (pp)
REVERT: B 1538 SER cc_start: 0.9437 (t) cc_final: 0.8997 (p)
REVERT: B 1672 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7793 (tt)
  outliers start: 30
  outliers final: 28
  residues processed: 87
  average time/residue: 0.0771
  time to fit residues: 10.5278
Evaluate side-chains
  91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  230 CYS
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  482 PHE
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  534 THR
Chi-restraints excluded: chain B residue  561 HIS
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  632 MET
Chi-restraints excluded: chain B residue  742 HIS
Chi-restraints excluded: chain B residue  779 GLU
Chi-restraints excluded: chain B residue  920 ILE
Chi-restraints excluded: chain B residue 1006 MET
Chi-restraints excluded: chain B residue 1395 LEU
Chi-restraints excluded: chain B residue 1441 GLU
Chi-restraints excluded: chain B residue 1461 SER
Chi-restraints excluded: chain B residue 1489 ILE
Chi-restraints excluded: chain B residue 1495 LEU
Chi-restraints excluded: chain B residue 1520 PHE
Chi-restraints excluded: chain B residue 1522 VAL
Chi-restraints excluded: chain B residue 1572 ILE
Chi-restraints excluded: chain B residue 1582 VAL
Chi-restraints excluded: chain B residue 1586 ASP
Chi-restraints excluded: chain B residue 1647 VAL
Chi-restraints excluded: chain B residue 1672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 110 optimal weight:    0.2980
   chunk 20 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 128 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 561 HIS
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.109513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.077055 restraints weight = 19951.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.080517 restraints weight = 10030.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.082750 restraints weight = 6800.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.084194 restraints weight = 5412.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.085097 restraints weight = 4707.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11647  Z= 0.164
  Angle     :  0.596   9.521  15959  Z= 0.304
  Chirality :  0.041   0.219   1743
  Planarity :  0.004   0.053   1855
  Dihedral  : 17.552 179.531   2217
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.35 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.70 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    Twisted General : 0.17 %

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: -1.02 (0.24), residues: 1244
  helix:  1.54 (0.30), residues: 321
  sheet: -1.01 (0.35), residues: 186
  loop : -1.68 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 559 
 TYR   0.008   0.001   TYR B 362 
 PHE   0.018   0.001   PHE B1520 
 TRP   0.008   0.001   TRP B 607 
 HIS   0.006   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (11637)
  covalent geometry    : angle       0.59420 (15953)
  hydrogen bonds       : bond        0.05603 (  318)
  hydrogen bonds       : angle       4.30506 (  926)
  metal coordination   : bond        0.00471 (   10)
  metal coordination   : angle       2.41861 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1554.26 seconds
wall clock time: 27 minutes 46.96 seconds (1666.96 seconds total)