Starting phenix.real_space_refine
on Mon Oct 26 03:47:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mys_48749/10_2026/9mys_48749.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mys_48749/10_2026/9mys_48749.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mys_48749/10_2026/9mys_48749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mys_48749/10_2026/9mys_48749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mys_48749/10_2026/9mys_48749.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mys_48749/10_2026/9mys_48749.cif"
  }
  resolution = 3.93
  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=  -0.006 sd=   0.978
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     298      5.49       5
     S      63      5.16       5
     C   11103      2.51       5
     N    3506      2.21       5
     O    4146      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 19120
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 6832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 887, 6832
          Classifications: {'peptide': 887}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 54, 'TRANS': 832}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 237
          Unresolved non-hydrogen angles: 290
          Unresolved non-hydrogen dihedrals: 201
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 9, 'ASP:plan': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 163
    Chain: "N"
      Number of atoms: 849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 849
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "O"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "P"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 812
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "Q"
      Number of atoms: 647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 647
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "X"
      Number of atoms: 3073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 3073
          Classifications: {'DNA': 149}
          Link IDs: {'rna3p': 148}
    Chain: "Y"
      Number of atoms: 3036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 3036
          Classifications: {'DNA': 149}
          Link IDs: {'rna3p': 148}
    Chain: "n"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 863
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "o"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 772
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "p"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 827
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "q"
      Number of atoms: 670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 670
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1, 'ML3:plan-1': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      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   5876  SG  CYS A1476      30.803  31.644 111.891  1.00227.60           S
  ATOM   5888  SG  CYS A1478      34.192  31.409 110.278  1.00195.35           S
  ATOM   5933  SG  CYS A1485      31.914  34.287 109.316  1.00354.86           S
  ATOM   1175  SG  CYS A 820      96.238  51.156 103.714  1.00197.82           S
  ATOM   1752  SG  CYS A 893      98.275  54.233 104.530  1.00222.69           S
  ATOM   1771  SG  CYS A 896      99.350  50.992 105.179  1.00191.57           S
  ATOM    300  SG  CYS A 653      33.362  48.289 115.395  1.00156.30           S
  ATOM    317  SG  CYS A 656      31.838  50.550 116.900  1.00139.04           S
  ATOM    339  SG  CYS A 659      30.785  50.354 113.697  1.00143.71           S
  ATOM    580  SG  CYS A 691      34.246  51.685 114.607  1.00142.62           S
  ATOM    379  SG  CYS A 664      20.142  60.626 113.087  1.00147.49           S
  ATOM    398  SG  CYS A 667      22.925  62.901 111.067  1.00146.79           S
  ATOM    418  SG  CYS A 670      20.769  59.646 109.798  1.00148.62           S
  ATOM    534  SG  CYS A 686      23.410  59.312 112.327  1.00158.86           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb="ZN    ZN A1704 " occ=0.32
  Time building chain proxies: 3.76, per 1000 atoms: 0.20
  Number of scatterers: 19120
  At special positions: 0
  Unit cell: (123.487, 122, 163.658, 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      63     16.00
     P     298     15.00
     O    4146      8.00
     N    3506      7.00
     C   11103      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: 4.45
  Conformation dependent library (CDL) restraints added in 596.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1701 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A1478 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A1485 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A1476 "
        pdb="ZN    ZN A1701 " - pdb=" NE2 HIS A1502 "
      pdb="  ZN A1702 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 896 "
        pdb="ZN    ZN A1702 " - pdb=" NE2 HIS A 793 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 893 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 820 "
      pdb="  ZN A1703 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 656 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 653 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 659 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 691 "
      pdb="  ZN A1704 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A 686 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A 664 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A 670 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A 667 "
      Number of angles added : 18


  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3124

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 17 sheets defined
      49.6% alpha, 10.7% beta
      147 base pairs and 251 stacking pairs defined.
    Time for finding SS restraints: 2.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 624 through 636
      removed outlier: 3.502A  pdb=" N   PHE A 628 " --> pdb=" O   VAL A 624 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLU A 634 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A 636 " --> pdb=" O   PHE A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
      removed outlier: 4.368A  pdb=" N   LYS A 644 " --> pdb=" O   ASP A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 661
    Processing helix  chain 'A' and resid 667 through 672
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.526A  pdb=" N   PHE A 676 " --> pdb=" O   MET A 673 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY A 677 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 673 through 677'
    Processing helix  chain 'A' and resid 805 through 809
    Processing helix  chain 'A' and resid 826 through 828
      No H-bonds generated for 'chain 'A' and resid 826 through 828'
    Processing helix  chain 'A' and resid 842 through 846
    Processing helix  chain 'A' and resid 850 through 855
      removed outlier: 3.835A  pdb=" N   LEU A 854 " --> pdb=" O   ASP A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 906
      removed outlier: 3.584A  pdb=" N   GLU A 906 " --> pdb=" O   MET A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 975
    Processing helix  chain 'A' and resid 1023 through 1027
    Processing helix  chain 'A' and resid 1030 through 1037
      removed outlier: 4.019A  pdb=" N   HIS A1036 " --> pdb=" O   PRO A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1056
      No H-bonds generated for 'chain 'A' and resid 1054 through 1056'
    Processing helix  chain 'A' and resid 1071 through 1079
      removed outlier: 4.104A  pdb=" N   GLY A1079 " --> pdb=" O   TYR A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1158
    Processing helix  chain 'A' and resid 1170 through 1181
    Processing helix  chain 'A' and resid 1190 through 1201
      removed outlier: 4.189A  pdb=" N   LEU A1194 " --> pdb=" O   ASP A1190 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A1195 " --> pdb=" O   CYS A1191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1245
      removed outlier: 4.127A  pdb=" N   ASN A1245 " --> pdb=" O   SER A1241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1246 through 1259
      removed outlier: 3.627A  pdb=" N   TYR A1258 " --> pdb=" O   TYR A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1270 through 1276
      removed outlier: 7.143A  pdb=" N   LYS A1275 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG A1276 " --> pdb=" O   SER A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1291
    Processing helix  chain 'A' and resid 1302 through 1305
      removed outlier: 3.844A  pdb=" N   GLY A1305 " --> pdb=" O   GLY A1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1302 through 1305'
    Processing helix  chain 'A' and resid 1335 through 1339
    Processing helix  chain 'A' and resid 1366 through 1372
    Processing helix  chain 'A' and resid 1394 through 1402
      removed outlier: 3.570A  pdb=" N   GLY A1402 " --> pdb=" O   ARG A1398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1418 through 1427
    Processing helix  chain 'A' and resid 1435 through 1439
    Processing helix  chain 'A' and resid 1476 through 1480
      removed outlier: 3.865A  pdb=" N   VAL A1479 " --> pdb=" O   CYS A1476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1498 through 1504
    Processing helix  chain 'A' and resid 1505 through 1511
      removed outlier: 3.877A  pdb=" N   ASN A1508 " --> pdb=" O   ASN A1505 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   HIS A1509 " --> pdb=" O   ARG A1506 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A1511 " --> pdb=" O   ASN A1508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1549 through 1557
    Processing helix  chain 'A' and resid 1568 through 1579
    Processing helix  chain 'A' and resid 1581 through 1600
      removed outlier: 3.618A  pdb=" N   CYS A1595 " --> pdb=" O   GLU A1591 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 16 through 21
    Processing helix  chain 'N' and resid 26 through 37
    Processing helix  chain 'N' and resid 45 through 74
      removed outlier: 4.337A  pdb=" N   VAL N  49 " --> pdb=" O   ALA N  45 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASN N  73 " --> pdb=" O   ALA N  69 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 79 through 90
    Processing helix  chain 'N' and resid 91 through 97
    Processing helix  chain 'N' and resid 112 through 116
      removed outlier: 3.593A  pdb=" N   LEU N 116 " --> pdb=" O   SER N 113 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 34 through 46
    Processing helix  chain 'O' and resid 52 through 81
      removed outlier: 4.059A  pdb=" N   ASN O  81 " --> pdb=" O   LEU O  77 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 87 through 99
      removed outlier: 3.672A  pdb=" N   ILE O  91 " --> pdb=" O   THR O  87 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 101 through 121
      removed outlier: 3.760A  pdb=" N   LYS O 105 " --> pdb=" O   GLY O 101 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 44 through 57
    Processing helix  chain 'P' and resid 63 through 79
      removed outlier: 3.812A  pdb=" N   ASP P  77 " --> pdb=" O   GLU P  73 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   PHE P  78 " --> pdb=" O   ILE P  74 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 85 through 114
    Processing helix  chain 'P' and resid 120 through 131
    Processing helix  chain 'Q' and resid 22 through 29
      removed outlier: 4.453A  pdb=" N   ILE Q  26 " --> pdb=" O   ARG Q  23 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE Q  29 " --> pdb=" O   ILE Q  26 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 30 through 42
    Processing helix  chain 'Q' and resid 49 through 76
      removed outlier: 4.142A  pdb=" N   GLU Q  53 " --> pdb=" O   LEU Q  49 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 82 through 94
    Processing helix  chain 'n' and resid 16 through 21
    Processing helix  chain 'n' and resid 26 through 37
    Processing helix  chain 'n' and resid 46 through 74
    Processing helix  chain 'n' and resid 79 through 90
      removed outlier: 3.911A  pdb=" N   ASP n  90 " --> pdb=" O   ALA n  86 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 91 through 97
    Processing helix  chain 'o' and resid 34 through 46
      removed outlier: 3.910A  pdb=" N   VAL o  38 " --> pdb=" O   TYR o  34 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR o  39 " --> pdb=" O   ALA o  35 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 52 through 81
      removed outlier: 3.508A  pdb=" N   ASN o  81 " --> pdb=" O   LEU o  77 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 87 through 99
      removed outlier: 3.541A  pdb=" N   ILE o  91 " --> pdb=" O   THR o  87 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU o  99 " --> pdb=" O   VAL o  95 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 102 through 120
    Processing helix  chain 'p' and resid 44 through 55
    Processing helix  chain 'p' and resid 63 through 79
      removed outlier: 3.902A  pdb=" N   ASP p  77 " --> pdb=" O   GLU p  73 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   PHE p  78 " --> pdb=" O   ILE p  74 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 85 through 114
      removed outlier: 3.584A  pdb=" N   ALA p 114 " --> pdb=" O   SER p 110 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 120 through 131
      removed outlier: 3.688A  pdb=" N   ARG p 131 " --> pdb=" O   ALA p 127 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 30 through 42
    Processing helix  chain 'q' and resid 49 through 76
      removed outlier: 4.207A  pdb=" N   GLU q  53 " --> pdb=" O   LEU q  49 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 82 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 751 through 752
    Processing sheet with id=AA2, first strand: chain 'A' and resid 814 through 824
      removed outlier: 7.127A  pdb=" N   VAL A 817 " --> pdb=" O   CYS A 798 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   CYS A 798 " --> pdb=" O   VAL A 817 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   GLU A 819 " --> pdb=" O   TRP A 796 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   MET A 791 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   LEU A 782 " --> pdb=" O   MET A 791 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   HIS A 793 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   LEU A 776 " --> pdb=" O   PHE A 797 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   CYS A 762 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER A 830 " --> pdb=" O   SER A 764 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 834 through 836
      removed outlier: 3.562A  pdb=" N   TYR A 865 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 868 through 870
    Processing sheet with id=AA5, first strand: chain 'A' and resid 909 through 916
      removed outlier: 7.095A  pdb=" N   SER A 925 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   GLN A 913 " --> pdb=" O   TYR A 923 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   TYR A 923 " --> pdb=" O   GLN A 913 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLU A 915 " --> pdb=" O   VAL A 921 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL A 921 " --> pdb=" O   GLU A 915 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE A 999 " --> pdb=" O   TYR A 923 " (cutoff:3.500A)
      removed outlier: 9.277A  pdb=" N   SER A 925 " --> pdb=" O   LYS A 997 " (cutoff:3.500A)
      removed outlier: 11.980A  pdb=" N   LYS A 997 " --> pdb=" O   SER A 925 " (cutoff:3.500A)
      removed outlier: 15.101A  pdb=" N   THR A 927 " --> pdb=" O   ARG A 995 " (cutoff:3.500A)
      removed outlier: 17.035A  pdb=" N   ARG A 995 " --> pdb=" O   THR A 927 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 916
      removed outlier: 7.095A  pdb=" N   SER A 925 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   GLN A 913 " --> pdb=" O   TYR A 923 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   TYR A 923 " --> pdb=" O   GLN A 913 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLU A 915 " --> pdb=" O   VAL A 921 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL A 921 " --> pdb=" O   GLU A 915 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 920 through 928
    current: chain 'A' and resid 1041 through 1052
      removed outlier: 4.112A  pdb=" N   LEU A1086 " --> pdb=" O   LEU A1042 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   TRP A1044 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ALA A1088 " --> pdb=" O   TRP A1044 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   ASP A1046 " --> pdb=" O   ALA A1088 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLY A1058 " --> pdb=" O   TYR A 940 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1187
      removed outlier: 8.670A  pdb=" N   THR A1185 " --> pdb=" O   ASP A1162 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU A1164 " --> pdb=" O   THR A1185 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   PHE A1187 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ALA A1166 " --> pdb=" O   PHE A1187 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   ASP A1143 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ALA A1166 " --> pdb=" O   ASP A1143 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ARG A1140 " --> pdb=" O   MET A1219 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   CYS A1221 " --> pdb=" O   ARG A1140 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   LEU A1142 " --> pdb=" O   CYS A1221 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU A1220 " --> pdb=" O   LEU A1264 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   GLU A1266 " --> pdb=" O   LEU A1220 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLY A1222 " --> pdb=" O   GLU A1266 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   VAL A1268 " --> pdb=" O   GLY A1222 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1343 through 1345
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1385 through 1387
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1444 through 1445
      removed outlier: 3.643A  pdb=" N   VAL A1444 " --> pdb=" O   ALA A1452 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 42 through 43
      removed outlier: 7.748A  pdb=" N   ARG N  42 " --> pdb=" O   ILE O  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'N' and resid 77 through 78
    Processing sheet with id=AB4, first strand: chain 'N' and resid 100 through 101
    Processing sheet with id=AB5, first strand: chain 'P' and resid 83 through 84
      removed outlier: 7.293A  pdb=" N   ARG P  83 " --> pdb=" O   VAL Q  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'n' and resid 42 through 43
      removed outlier: 7.781A  pdb=" N   ARG n  42 " --> pdb=" O   ILE o  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'n' and resid 77 through 78
    Processing sheet with id=AB8, first strand: chain 'p' and resid 83 through 84
      removed outlier: 6.833A  pdb=" N   ARG p  83 " --> pdb=" O   VAL q  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8

    596 hydrogen bonds defined for protein.
    1695 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      377 hydrogen bonds
      754 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      251 stacking parallelities
  Total time for adding SS restraints: 7.19

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5120
        1.34 -     1.46: 5268
        1.46 -     1.58: 9025
        1.58 -     1.70: 594
        1.70 -     1.82: 94
  Bond restraints: 20101
  Sorted by residual:
  bond pdb=" C3'  DT Y 164 "
       pdb=" C2'  DT Y 164 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.22e+01
  bond pdb=" C3'  DG X  91 "
       pdb=" C2'  DG X  91 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.21e+01
  bond pdb=" C3'  DG Y  23 "
       pdb=" C2'  DG Y  23 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.18e+01
  bond pdb=" C3'  DT Y  17 "
       pdb=" C2'  DT Y  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.17e+01
  bond pdb=" N   PRO p  38 "
       pdb=" CD  PRO p  38 "
    ideal  model  delta    sigma   weight residual
    1.473  1.519 -0.046 1.40e-02 5.10e+03 1.08e+01
  ... (remaining 20096 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 27926
        2.51 -     5.02: 465
        5.02 -     7.53: 53
        7.53 -    10.04: 21
       10.04 -    12.55: 8
  Bond angle restraints: 28473
  Sorted by residual:
  angle pdb=" CA  PRO p  38 "
        pdb=" N   PRO p  38 "
        pdb=" CD  PRO p  38 "
      ideal   model   delta    sigma   weight residual
     112.00   99.77   12.23 1.40e+00 5.10e-01 7.63e+01
  angle pdb=" CA  LYS A 666 "
        pdb=" CB  LYS A 666 "
        pdb=" CG  LYS A 666 "
      ideal   model   delta    sigma   weight residual
     114.10  123.53   -9.43 2.00e+00 2.50e-01 2.22e+01
  angle pdb=" N3   DT Y  26 "
        pdb=" C4   DT Y  26 "
        pdb=" O4   DT Y  26 "
      ideal   model   delta    sigma   weight residual
     119.90  122.58   -2.68 6.00e-01 2.78e+00 1.99e+01
  angle pdb=" C   ASN N  73 "
        pdb=" N   LYS N  74 "
        pdb=" CA  LYS N  74 "
      ideal   model   delta    sigma   weight residual
     122.36  128.80   -6.44 1.47e+00 4.63e-01 1.92e+01
  angle pdb=" CA  MET A 845 "
        pdb=" CB  MET A 845 "
        pdb=" CG  MET A 845 "
      ideal   model   delta    sigma   weight residual
     114.10  122.80   -8.70 2.00e+00 2.50e-01 1.89e+01
  ... (remaining 28468 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.37: 9865
       35.37 -    70.74: 1449
       70.74 -   106.11: 21
      106.11 -   141.48: 0
      141.48 -   176.85: 2
  Dihedral angle restraints: 11337
    sinusoidal: 6492
      harmonic: 4845
  Sorted by residual:
  dihedral pdb=" CA  TYR A1292 "
           pdb=" C   TYR A1292 "
           pdb=" N   GLN A1293 "
           pdb=" CA  GLN A1293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LEU p  60 "
           pdb=" C   LEU p  60 "
           pdb=" N   LEU p  61 "
           pdb=" CA  LEU p  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.55  -20.45     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  ILE Q  29 "
           pdb=" C   ILE Q  29 "
           pdb=" N   THR Q  30 "
           pdb=" CA  THR Q  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.97  -20.03     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 11334 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 2326
       0.047 -    0.095: 674
       0.095 -    0.142: 176
       0.142 -    0.189: 13
       0.189 -    0.236: 4
  Chirality restraints: 3193
  Sorted by residual:
  chirality pdb=" CG  LEU p  92 "
            pdb=" CB  LEU p  92 "
            pdb=" CD1 LEU p  92 "
            pdb=" CD2 LEU p  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CG  LEU o  42 "
            pdb=" CB  LEU o  42 "
            pdb=" CD1 LEU o  42 "
            pdb=" CD2 LEU o  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CG  LEU A1590 "
            pdb=" CB  LEU A1590 "
            pdb=" CD1 LEU A1590 "
            pdb=" CD2 LEU A1590 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.34e-01
  ... (remaining 3190 not shown)

  Planarity restraints: 2620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS p  37 "   -0.115 5.00e-02 4.00e+02   1.62e-01 4.21e+01
        pdb=" N   PRO p  38 "    0.280 5.00e-02 4.00e+02
        pdb=" CA  PRO p  38 "   -0.087 5.00e-02 4.00e+02
        pdb=" CD  PRO p  38 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1436 "   -0.023 2.00e-02 2.50e+03   2.40e-02 1.43e+01
        pdb=" CG  TRP A1436 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1436 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1436 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1436 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1436 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1436 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1436 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1436 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1436 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG p 134 "   -0.315 9.50e-02 1.11e+02   1.41e-01 1.25e+01
        pdb=" NE  ARG p 134 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG p 134 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG p 134 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG p 134 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2617 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 329
        2.65 -     3.21: 17040
        3.21 -     3.77: 34680
        3.77 -     4.34: 44063
        4.34 -     4.90: 64667
  Nonbonded interactions: 160779
  Sorted by model distance:
  nonbonded pdb=" OH  TYR n  50 "
            pdb=" OE1 GLN o  92 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" O   TYR N  39 "
            pdb=" OG  SER O  75 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OH  TYR O  80 "
            pdb=" OD1 ASP Q  85 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" N   ASP q  24 "
            pdb=" OD1 ASP q  24 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" O   SER A1237 "
            pdb=" OG  SER A1241 "
     model   vdw
     2.160 3.040
  ... (remaining 160774 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'N' and (resid 10 or (resid 11 through 12 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 13 through 119 or (resid 120 and (name N or n \ 
ame CA or name C or name O or name CB ))))
  selection = (chain 'n' and resid 10 through 120)
}
ncs_group {
  reference = (chain 'O' and (resid 28 through 30 or (resid 31 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 32 through 121))
  selection = (chain 'o' and resid 28 through 121)
}
ncs_group {
  reference = (chain 'P' and resid 36 through 134)
  selection = (chain 'p' and ((resid 36 through 37 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 38 through 41 or (resid 42 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 43 through 134))
}
ncs_group {
  reference = chain 'Q'
  selection = (chain 'q' and (resid 21 through 22 or (resid 23 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 24 through 102))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.32 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:             1.840
  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:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     26.100
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
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   0.507  20117  Z= 0.482
  Angle     :  0.873  12.550  28491  Z= 0.622
  Chirality :  0.047   0.236   3193
  Planarity :  0.007   0.162   2620
  Dihedral  : 24.456 176.846   8213
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 23.94 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.21), residues: 1643
  helix:  0.61 (0.20), residues: 721
  sheet: -0.54 (0.41), residues: 142
  loop : -0.36 (0.22), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A1574 
 TYR   0.030   0.002   TYR Q  88 
 PHE   0.029   0.002   PHE A 628 
 TRP   0.064   0.003   TRP A1436 
 HIS   0.008   0.001   HIS A1459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00531 /  0.44 (20101)
  covalent geometry    : angle       0.86876 /  0.62 (28473)
  hydrogen bonds       : bond        0.11754 /  7.75 (  970)
  hydrogen bonds       : angle       5.11250 /  3.47 ( 2449)
  metal coordination   : bond        0.22219 / 12.06 (   16)
  metal coordination   : angle       3.60277 /  1.94 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: A 1417 MET cc_start: -0.0889 (ptp) cc_final: -0.1143 (ptt)
REVERT: A 1533 MET cc_start: -0.2673 (OUTLIER) cc_final: -0.3218 (mmt)
REVERT: P   73 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7512 (tm-30)
REVERT: n   36 LYS cc_start: 0.8389 (tppt) cc_final: 0.8081 (tttm)
REVERT: n   57 TYR cc_start: 0.8417 (t80) cc_final: 0.8049 (t80)
REVERT: o   80 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6985 (m-80)
REVERT: o   90 GLU cc_start: 0.7867 (mp0) cc_final: 0.7461 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 150
  average time/residue: 0.1467
  time to fit residues: 33.3519
Evaluate side-chains
  142 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1232 MET
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1533 MET
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain p residue   81 ASP
Chi-restraints excluded: chain q residue   24 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149]
   chunk 98 optimal weight:    0.0970
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.0980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
n 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.140647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.108646 restraints weight = 55030.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.107588 restraints weight = 64498.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.108875 restraints weight = 51961.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.108161 restraints weight = 37025.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.108491 restraints weight = 34774.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3762 r_free = 0.3762    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3762 r_free = 0.3762    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  20117  Z= 0.211
  Angle     :  0.751  17.762  28491  Z= 0.403
  Chirality :  0.045   0.329   3193
  Planarity :  0.006   0.056   2620
  Dihedral  : 27.330 178.426   5125
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 17.87 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.20), residues: 1643
  helix:  0.74 (0.19), residues: 748
  sheet: -0.44 (0.41), residues: 143
  loop : -0.42 (0.23), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1574 
 TYR   0.034   0.002   TYR Q  88 
 PHE   0.015   0.002   PHE A 628 
 TRP   0.021   0.002   TRP A1436 
 HIS   0.005   0.001   HIS A1459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.21 (20101)
  covalent geometry    : angle       0.72786 /  0.40 (28473)
  hydrogen bonds       : bond        0.05545 /  3.72 (  970)
  hydrogen bonds       : angle       4.26592 /  2.88 ( 2449)
  metal coordination   : bond        0.03077 /  1.96 (   16)
  metal coordination   : angle       7.34645 /  5.48 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 124
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: -0.1262 (ptp) cc_final: -0.1804 (ptt)
REVERT: P   51 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.7911 (tp)
REVERT: n   36 LYS cc_start: 0.8680 (tppt) cc_final: 0.8045 (tttm)
REVERT: n   95 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8285 (mttm)
REVERT: o   80 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6823 (m-80)
REVERT: p   90 MET cc_start: 0.8097 (mmm) cc_final: 0.7770 (mmm)
  outliers start: 50
  outliers final: 30
  residues processed: 166
  average time/residue: 0.1279
  time to fit residues: 33.0621
Evaluate side-chains
  142 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  664 CYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1479 VAL
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1538 ARG
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   76 THR
Chi-restraints excluded: chain O residue   36 ILE
Chi-restraints excluded: chain O residue   87 THR
Chi-restraints excluded: chain O residue  108 VAL
Chi-restraints excluded: chain O residue  119 THR
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   77 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain o residue   85 THR
Chi-restraints excluded: chain p residue   45 THR
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain q residue   24 ASP
Chi-restraints excluded: chain q residue   30 THR
Chi-restraints excluded: chain q residue   43 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [188, 46, 8, 178, 27, 10, 112, 95, 2, 71, 68]
   chunk 188 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 178 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 112 optimal weight:    0.6980
   chunk 95 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 913 GLN
A1508 ASN
O  44 GLN
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
n 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.141802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.112622 restraints weight = 55329.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.111614 restraints weight = 80583.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.112364 restraints weight = 61190.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.112387 restraints weight = 41349.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.112556 restraints weight = 40717.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  20117  Z= 0.151
  Angle     :  0.648  13.102  28491  Z= 0.360
  Chirality :  0.042   0.338   3193
  Planarity :  0.004   0.048   2620
  Dihedral  : 27.316 179.733   5116
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.53 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.21), residues: 1643
  helix:  1.03 (0.19), residues: 750
  sheet: -0.19 (0.44), residues: 127
  loop : -0.38 (0.22), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1574 
 TYR   0.029   0.002   TYR q  88 
 PHE   0.024   0.001   PHE A 797 
 TRP   0.011   0.001   TRP A1498 
 HIS   0.004   0.001   HIS Q  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.15 (20101)
  covalent geometry    : angle       0.63759 /  0.36 (28473)
  hydrogen bonds       : bond        0.04759 /  3.19 (  970)
  hydrogen bonds       : angle       4.06133 /  2.74 ( 2449)
  metal coordination   : bond        0.01016 /  0.53 (   16)
  metal coordination   : angle       4.64114 /  3.02 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 131
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: -0.1112 (ptp) cc_final: -0.1749 (ptt)
REVERT: P   51 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: Q   84 MET cc_start: 0.8293 (tpp) cc_final: 0.7939 (tpp)
REVERT: n   36 LYS cc_start: 0.8669 (tppt) cc_final: 0.8128 (tttt)
REVERT: n   95 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8240 (mttm)
REVERT: o   80 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6744 (m-80)
REVERT: p   90 MET cc_start: 0.7992 (mmm) cc_final: 0.7646 (mmm)
  outliers start: 47
  outliers final: 29
  residues processed: 170
  average time/residue: 0.1311
  time to fit residues: 34.4608
Evaluate side-chains
  149 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  664 CYS
Chi-restraints excluded: chain A residue  675 LYS
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1538 ARG
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain O residue   87 THR
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain n residue  104 GLN
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   77 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   80 THR
Chi-restraints excluded: chain q residue   30 THR
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   72 TYR
Chi-restraints excluded: chain q residue   86 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [38, 18, 17, 24, 177, 31, 36, 20, 83, 27, 111]
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0270
   chunk 24 optimal weight:   10.0000
   chunk 177 optimal weight:    0.3980
   chunk 31 optimal weight:    6.9990
   chunk 36 optimal weight:   20.0000
   chunk 20 optimal weight:    0.7980
   chunk 83 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.6038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  55 GLN
n 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.142070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.112387 restraints weight = 54975.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.111377 restraints weight = 77207.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.112258 restraints weight = 61710.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.111952 restraints weight = 44694.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.112207 restraints weight = 39214.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  20117  Z= 0.141
  Angle     :  0.632  10.959  28491  Z= 0.352
  Chirality :  0.041   0.335   3193
  Planarity :  0.004   0.048   2620
  Dihedral  : 27.334 179.555   5114
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 18.83 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.21), residues: 1643
  helix:  1.09 (0.19), residues: 753
  sheet: -0.47 (0.43), residues: 134
  loop : -0.30 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 650 
 TYR   0.024   0.002   TYR q  88 
 PHE   0.027   0.002   PHE A 797 
 TRP   0.010   0.001   TRP A1498 
 HIS   0.008   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.14 (20101)
  covalent geometry    : angle       0.62257 /  0.35 (28473)
  hydrogen bonds       : bond        0.04563 /  3.07 (  970)
  hydrogen bonds       : angle       3.93327 /  2.65 ( 2449)
  metal coordination   : bond        0.00861 /  0.45 (   16)
  metal coordination   : angle       4.38230 /  2.81 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 129
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: -0.1159 (ptp) cc_final: -0.1827 (ptt)
REVERT: P   51 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7849 (tp)
REVERT: n   36 LYS cc_start: 0.8695 (tppt) cc_final: 0.8123 (tttt)
REVERT: n   95 LYS cc_start: 0.8694 (tmmt) cc_final: 0.8251 (mttm)
REVERT: n  104 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6599 (mp10)
REVERT: o   80 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6848 (m-80)
REVERT: p   90 MET cc_start: 0.7993 (mmm) cc_final: 0.7653 (mmm)
REVERT: q   88 TYR cc_start: 0.4565 (t80) cc_final: 0.4257 (t80)
  outliers start: 50
  outliers final: 26
  residues processed: 171
  average time/residue: 0.1330
  time to fit residues: 35.1154
Evaluate side-chains
  153 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  664 CYS
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1538 ARG
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain O residue  108 VAL
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain n residue   51 LEU
Chi-restraints excluded: chain n residue   59 THR
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain n residue  104 GLN
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain q residue   30 THR
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   72 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [40, 120, 1, 94, 125, 79, 26, 44, 185, 145, 86]
   chunk 40 optimal weight:    0.0030
   chunk 120 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 125 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 26 optimal weight:    0.0870
   chunk 44 optimal weight:    9.9990
   chunk 185 optimal weight:    0.8980
   chunk 145 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   overall best weight:    0.4568

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 635 GLN
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
p  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.142783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.114654 restraints weight = 55132.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.113547 restraints weight = 83498.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.114317 restraints weight = 64479.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.114214 restraints weight = 43860.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.114429 restraints weight = 42534.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  20117  Z= 0.135
  Angle     :  0.619  12.478  28491  Z= 0.345
  Chirality :  0.041   0.334   3193
  Planarity :  0.004   0.049   2620
  Dihedral  : 27.326 179.744   5114
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.75 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.21), residues: 1643
  helix:  1.13 (0.19), residues: 754
  sheet: -0.47 (0.43), residues: 134
  loop : -0.34 (0.23), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1285 
 TYR   0.020   0.001   TYR q  88 
 PHE   0.033   0.001   PHE A 797 
 TRP   0.009   0.001   TRP A1498 
 HIS   0.006   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.13 (20101)
  covalent geometry    : angle       0.60733 /  0.34 (28473)
  hydrogen bonds       : bond        0.04413 /  2.97 (  970)
  hydrogen bonds       : angle       3.87301 /  2.62 ( 2449)
  metal coordination   : bond        0.00886 /  0.50 (   16)
  metal coordination   : angle       4.77286 /  3.72 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  650 ARG cc_start: 0.6659 (ptt90) cc_final: 0.6162 (ptt90)
REVERT: A  694 MET cc_start: 0.6828 (tpp) cc_final: 0.6522 (tpp)
REVERT: A  845 MET cc_start: 0.6644 (ppp) cc_final: 0.6430 (ppp)
REVERT: A 1371 MET cc_start: 0.3560 (pmm) cc_final: 0.3216 (mpp)
REVERT: A 1417 MET cc_start: -0.1604 (ptp) cc_final: -0.2606 (ptt)
REVERT: P   51 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.7866 (tp)
REVERT: P  126 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (tp)
REVERT: n   36 LYS cc_start: 0.8654 (tppt) cc_final: 0.8154 (tttt)
REVERT: n   95 LYS cc_start: 0.8556 (tmmt) cc_final: 0.8148 (mmtm)
REVERT: o   80 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6971 (m-80)
REVERT: o   92 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8639 (tt0)
REVERT: p   83 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7525 (ptp-170)
REVERT: p   90 MET cc_start: 0.7929 (mmm) cc_final: 0.7509 (mmm)
REVERT: q   88 TYR cc_start: 0.4495 (t80) cc_final: 0.4195 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 160
  average time/residue: 0.1490
  time to fit residues: 35.7522
Evaluate side-chains
  149 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1538 ARG
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain P residue  126 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain n residue   51 LEU
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain o residue   92 GLN
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   83 ARG
Chi-restraints excluded: chain q residue   30 THR
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   72 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [33, 48, 41, 147, 176, 141, 171, 77, 164, 32, 13]
   chunk 33 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 147 optimal weight:    9.9990
   chunk 176 optimal weight:    2.9990
   chunk 141 optimal weight:   20.0000
   chunk 171 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 164 optimal weight:    0.0870
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.4166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 626 GLN
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
n  73 ASN
n 104 GLN
q  75 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.137467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.105829 restraints weight = 54085.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.104389 restraints weight = 69074.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.105117 restraints weight = 57912.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.105180 restraints weight = 39439.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.105362 restraints weight = 38030.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  20117  Z= 0.249
  Angle     :  0.731  12.673  28491  Z= 0.392
  Chirality :  0.046   0.409   3193
  Planarity :  0.006   0.078   2620
  Dihedral  : 27.758 179.197   5114
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 19.72 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.21), residues: 1643
  helix:  0.91 (0.19), residues: 747
  sheet: -0.70 (0.44), residues: 135
  loop : -0.35 (0.23), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1285 
 TYR   0.029   0.002   TYR q  88 
 PHE   0.022   0.002   PHE A 797 
 TRP   0.008   0.001   TRP A1498 
 HIS   0.007   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00546 /  0.25 (20101)
  covalent geometry    : angle       0.71545 /  0.39 (28473)
  hydrogen bonds       : bond        0.05657 /  3.78 (  970)
  hydrogen bonds       : angle       4.12239 /  2.79 ( 2449)
  metal coordination   : bond        0.02469 /  1.47 (   16)
  metal coordination   : angle       6.04706 /  4.22 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 119
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  694 MET cc_start: 0.6926 (tpp) cc_final: 0.6636 (tpp)
REVERT: A  780 THR cc_start: 0.1212 (OUTLIER) cc_final: 0.0976 (m)
REVERT: A  881 LYS cc_start: 0.3173 (OUTLIER) cc_final: 0.2958 (mptt)
REVERT: A 1417 MET cc_start: -0.0831 (ptp) cc_final: -0.2023 (ptt)
REVERT: N   71 ARG cc_start: 0.5937 (mtt90) cc_final: 0.5300 (mtm-85)
REVERT: P   51 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8078 (tp)
REVERT: n   95 LYS cc_start: 0.8731 (tmmt) cc_final: 0.8487 (tttp)
REVERT: o   92 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8595 (tp-100)
REVERT: p   83 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7626 (ptp-170)
REVERT: p   90 MET cc_start: 0.8139 (mmm) cc_final: 0.7895 (tpp)
REVERT: q   35 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7265 (ttp80)
  outliers start: 54
  outliers final: 34
  residues processed: 163
  average time/residue: 0.1394
  time to fit residues: 34.7999
Evaluate side-chains
  150 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 110
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  675 LYS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  792 PHE
Chi-restraints excluded: chain A residue  830 SER
Chi-restraints excluded: chain A residue  881 LYS
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   87 VAL
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue   62 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain n residue   16 THR
Chi-restraints excluded: chain n residue   59 THR
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain o residue   85 THR
Chi-restraints excluded: chain o residue   92 GLN
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   83 ARG
Chi-restraints excluded: chain q residue   30 THR
Chi-restraints excluded: chain q residue   35 ARG
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   72 TYR
Chi-restraints excluded: chain q residue   86 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [87, 33, 128, 155, 108, 62, 41, 96, 64, 167, 171]
   chunk 87 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 128 optimal weight:   20.0000
   chunk 155 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0050
   chunk 62 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 64 optimal weight:   30.0000
   chunk 167 optimal weight:    4.9990
   chunk 171 optimal weight:    0.5980
   overall best weight:    0.5994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 790 GLN
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  81 ASN
** P  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 108 ASN
n  73 ASN
p  93 GLN
q  75 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.140043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.109880 restraints weight = 54364.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.108688 restraints weight = 74176.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.109613 restraints weight = 58214.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.109445 restraints weight = 38568.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.109680 restraints weight = 38262.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  20117  Z= 0.142
  Angle     :  0.634  10.568  28491  Z= 0.349
  Chirality :  0.042   0.373   3193
  Planarity :  0.004   0.058   2620
  Dihedral  : 27.561 178.318   5114
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.05 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.21), residues: 1643
  helix:  1.08 (0.19), residues: 747
  sheet: -0.73 (0.44), residues: 134
  loop : -0.32 (0.23), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  72 
 TYR   0.024   0.001   TYR q  88 
 PHE   0.021   0.001   PHE A 797 
 TRP   0.012   0.001   TRP A 783 
 HIS   0.005   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.14 (20101)
  covalent geometry    : angle       0.62122 /  0.35 (28473)
  hydrogen bonds       : bond        0.04546 /  3.05 (  970)
  hydrogen bonds       : angle       3.90470 /  2.64 ( 2449)
  metal coordination   : bond        0.01137 /  0.62 (   16)
  metal coordination   : angle       4.97972 /  3.39 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  694 MET cc_start: 0.6947 (tpp) cc_final: 0.6690 (tpp)
REVERT: A  881 LYS cc_start: 0.3216 (OUTLIER) cc_final: 0.2955 (mptt)
REVERT: A 1417 MET cc_start: -0.1404 (ptp) cc_final: -0.2527 (ptt)
REVERT: O   42 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6731 (tp)
REVERT: P   51 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8283 (tp)
REVERT: P  126 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: n   95 LYS cc_start: 0.8572 (tmmt) cc_final: 0.8210 (mmtm)
REVERT: o   27 ARG cc_start: 0.4869 (tpt-90) cc_final: 0.4453 (mmm160)
REVERT: o   80 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.7047 (m-80)
REVERT: o   92 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8627 (tt0)
REVERT: p   90 MET cc_start: 0.7947 (mmm) cc_final: 0.7660 (tpp)
REVERT: q   35 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7039 (ttp80)
  outliers start: 44
  outliers final: 26
  residues processed: 163
  average time/residue: 0.1449
  time to fit residues: 35.5960
Evaluate side-chains
  153 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  792 PHE
Chi-restraints excluded: chain A residue  830 SER
Chi-restraints excluded: chain A residue  881 LYS
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1538 ARG
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain O residue   42 LEU
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain P residue  126 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain n residue   59 THR
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain o residue   92 GLN
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   74 ILE
Chi-restraints excluded: chain q residue   35 ARG
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   86 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [26, 70, 125, 40, 64, 145, 185, 18, 77, 180, 172]
   chunk 26 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 145 optimal weight:   10.0000
   chunk 185 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 180 optimal weight:    0.9980
   chunk 172 optimal weight:    1.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.138432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.108644 restraints weight = 54420.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.106793 restraints weight = 92513.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.107834 restraints weight = 71089.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.107945 restraints weight = 48747.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.108347 restraints weight = 45571.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  20117  Z= 0.187
  Angle     :  0.680  10.654  28491  Z= 0.367
  Chirality :  0.043   0.374   3193
  Planarity :  0.005   0.052   2620
  Dihedral  : 27.711 178.369   5113
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.20 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.21), residues: 1643
  helix:  1.02 (0.19), residues: 747
  sheet: -0.81 (0.44), residues: 128
  loop : -0.34 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1555 
 TYR   0.015   0.002   TYR q  88 
 PHE   0.018   0.001   PHE A 628 
 TRP   0.007   0.001   TRP A 783 
 HIS   0.005   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.19 (20101)
  covalent geometry    : angle       0.66553 /  0.37 (28473)
  hydrogen bonds       : bond        0.04964 /  3.33 (  970)
  hydrogen bonds       : angle       3.99519 /  2.70 ( 2449)
  metal coordination   : bond        0.01051 /  0.55 (   16)
  metal coordination   : angle       5.53840 /  3.69 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 118
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  791 MET cc_start: -0.2223 (mmt) cc_final: -0.2763 (tpt)
REVERT: A 1417 MET cc_start: -0.1263 (ptp) cc_final: -0.2390 (ptt)
REVERT: P   51 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8287 (tp)
REVERT: P  126 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8790 (tp)
REVERT: n   95 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8482 (tttp)
REVERT: o   27 ARG cc_start: 0.5010 (tpt-90) cc_final: 0.4436 (mmm160)
REVERT: o   80 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7287 (m-80)
REVERT: o   92 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8508 (tp-100)
REVERT: p   90 MET cc_start: 0.8137 (mmm) cc_final: 0.7879 (tpp)
REVERT: q   35 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7154 (ttp80)
  outliers start: 41
  outliers final: 31
  residues processed: 151
  average time/residue: 0.1434
  time to fit residues: 32.5492
Evaluate side-chains
  149 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  664 CYS
Chi-restraints excluded: chain A residue  675 LYS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  792 PHE
Chi-restraints excluded: chain A residue  830 SER
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain P residue  126 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain n residue   59 THR
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   80 TYR
Chi-restraints excluded: chain o residue   85 THR
Chi-restraints excluded: chain o residue   92 GLN
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   74 ILE
Chi-restraints excluded: chain q residue   35 ARG
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   72 TYR
Chi-restraints excluded: chain q residue   86 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [113, 12, 186, 26, 80, 45, 134, 173, 156, 133, 110]
   chunk 113 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 186 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 80 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 134 optimal weight:   10.0000
   chunk 173 optimal weight:    0.7980
   chunk 156 optimal weight:    0.9990
   chunk 133 optimal weight:   10.0000
   chunk 110 optimal weight:    0.3980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
q  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.139707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.110328 restraints weight = 54282.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.109216 restraints weight = 81263.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.109802 restraints weight = 64198.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.109543 restraints weight = 44898.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.109764 restraints weight = 40757.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  20117  Z= 0.144
  Angle     :  0.637  10.007  28491  Z= 0.349
  Chirality :  0.042   0.363   3193
  Planarity :  0.004   0.051   2620
  Dihedral  : 27.613 178.215   5113
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.79 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.21), residues: 1643
  helix:  1.12 (0.19), residues: 748
  sheet: -0.79 (0.44), residues: 128
  loop : -0.32 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 650 
 TYR   0.021   0.001   TYR O  37 
 PHE   0.021   0.001   PHE A 628 
 TRP   0.006   0.001   TRP A 843 
 HIS   0.005   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 (20101)
  covalent geometry    : angle       0.62512 /  0.35 (28473)
  hydrogen bonds       : bond        0.04511 /  3.02 (  970)
  hydrogen bonds       : angle       3.92162 /  2.64 ( 2449)
  metal coordination   : bond        0.00717 /  0.40 (   16)
  metal coordination   : angle       4.86261 /  3.29 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  791 MET cc_start: -0.2014 (mmt) cc_final: -0.2560 (tpt)
REVERT: A 1417 MET cc_start: -0.1360 (ptp) cc_final: -0.2488 (ptt)
REVERT: O   42 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.7014 (tp)
REVERT: P   51 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8211 (tp)
REVERT: P  126 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8792 (tp)
REVERT: n   95 LYS cc_start: 0.8692 (tmmt) cc_final: 0.8373 (tttp)
REVERT: o   27 ARG cc_start: 0.4955 (tpt-90) cc_final: 0.4378 (mmm160)
REVERT: o   92 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8674 (tt0)
REVERT: o  102 GLU cc_start: 0.7150 (pm20) cc_final: 0.6902 (pm20)
REVERT: p   90 MET cc_start: 0.7975 (mmm) cc_final: 0.7685 (tpp)
REVERT: q   35 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7083 (ttp80)
  outliers start: 34
  outliers final: 25
  residues processed: 153
  average time/residue: 0.1342
  time to fit residues: 31.8041
Evaluate side-chains
  145 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 CYS
Chi-restraints excluded: chain A residue  792 PHE
Chi-restraints excluded: chain A residue  830 SER
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain O residue   42 LEU
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain P residue  126 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain n residue   59 THR
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   92 GLN
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   74 ILE
Chi-restraints excluded: chain q residue   35 ARG
Chi-restraints excluded: chain q residue   43 VAL
Chi-restraints excluded: chain q residue   86 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [4, 89, 167, 10, 141, 14, 55, 127, 37, 30, 165]
   chunk 4 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 167 optimal weight:    0.0050
   chunk 10 optimal weight:    7.9990
   chunk 141 optimal weight:   20.0000
   chunk 14 optimal weight:    0.0570
   chunk 55 optimal weight:    5.9990
   chunk 127 optimal weight:   30.0000
   chunk 37 optimal weight:    0.0170
   chunk 30 optimal weight:    9.9990
   chunk 165 optimal weight:    9.9990
   overall best weight:    1.6154

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N  73 ASN
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.138057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.108347 restraints weight = 54287.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.107014 restraints weight = 79219.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.107987 restraints weight = 67238.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.107479 restraints weight = 49676.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.107909 restraints weight = 43584.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  20117  Z= 0.187
  Angle     :  0.686  10.238  28491  Z= 0.370
  Chirality :  0.043   0.375   3193
  Planarity :  0.005   0.053   2620
  Dihedral  : 27.756 177.813   5111
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.24 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.21), residues: 1643
  helix:  1.03 (0.19), residues: 752
  sheet: -0.81 (0.44), residues: 128
  loop : -0.34 (0.23), residues: 763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG o  76 
 TYR   0.019   0.002   TYR Q  98 
 PHE   0.018   0.001   PHE A 628 
 TRP   0.007   0.001   TRP A 843 
 HIS   0.005   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.19 (20101)
  covalent geometry    : angle       0.67429 /  0.37 (28473)
  hydrogen bonds       : bond        0.04939 /  3.32 (  970)
  hydrogen bonds       : angle       4.01084 /  2.70 ( 2449)
  metal coordination   : bond        0.00826 /  0.45 (   16)
  metal coordination   : angle       5.15627 /  3.50 (   18)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  791 MET cc_start: -0.2036 (mmt) cc_final: -0.2549 (tpt)
REVERT: A 1417 MET cc_start: -0.1264 (ptp) cc_final: -0.2356 (ptt)
REVERT: O   42 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7246 (tp)
REVERT: O   56 MET cc_start: 0.7429 (tpt) cc_final: 0.6639 (tpt)
REVERT: P   51 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8349 (tp)
REVERT: P  126 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8836 (tp)
REVERT: n   95 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8463 (tttp)
REVERT: o   27 ARG cc_start: 0.5021 (tpt-90) cc_final: 0.4421 (mmm160)
REVERT: o   92 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8468 (tp-100)
REVERT: p   90 MET cc_start: 0.8079 (mmm) cc_final: 0.7823 (tpp)
REVERT: q   35 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7219 (ttp80)
  outliers start: 36
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1377
  time to fit residues: 30.5468
Evaluate side-chains
  145 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 CYS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  792 PHE
Chi-restraints excluded: chain A residue  830 SER
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1278 MET
Chi-restraints excluded: chain A residue 1386 ILE
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1527 VAL
Chi-restraints excluded: chain A residue 1562 THR
Chi-restraints excluded: chain N residue   79 ILE
Chi-restraints excluded: chain O residue   42 LEU
Chi-restraints excluded: chain P residue   51 ILE
Chi-restraints excluded: chain P residue  109 LEU
Chi-restraints excluded: chain P residue  126 LEU
Chi-restraints excluded: chain Q residue   30 THR
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   73 THR
Chi-restraints excluded: chain n residue   59 THR
Chi-restraints excluded: chain n residue   61 GLU
Chi-restraints excluded: chain n residue   99 ARG
Chi-restraints excluded: chain n residue  101 THR
Chi-restraints excluded: chain o residue   42 LEU
Chi-restraints excluded: chain o residue   85 THR
Chi-restraints excluded: chain o residue   92 GLN
Chi-restraints excluded: chain p residue   57 SER
Chi-restraints excluded: chain p residue   74 ILE
Chi-restraints excluded: chain q residue   35 ARG
Chi-restraints excluded: chain q residue   43 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks: [159, 34, 114, 57, 189, 72, 177, 135, 175, 35, 183]
   chunk 159 optimal weight:    0.0470
   chunk 34 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 189 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 177 optimal weight:    0.6980
   chunk 135 optimal weight:    9.9990
   chunk 175 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 183 optimal weight:    0.0270
   overall best weight:    0.4536

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.140051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.109756 restraints weight = 54435.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.108734 restraints weight = 63142.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.109699 restraints weight = 55017.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.109478 restraints weight = 37291.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.109823 restraints weight = 35308.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20117  Z= 0.137
  Angle     :  0.645   9.966  28491  Z= 0.352
  Chirality :  0.042   0.354   3193
  Planarity :  0.004   0.051   2620
  Dihedral  : 27.594 178.276   5111
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.91 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.21), residues: 1643
  helix:  1.15 (0.19), residues: 750
  sheet: -0.79 (0.44), residues: 128
  loop : -0.30 (0.23), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 651 
 TYR   0.021   0.002   TYR O  37 
 PHE   0.021   0.001   PHE A 628 
 TRP   0.007   0.001   TRP A 843 
 HIS   0.005   0.001   HIS P 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.14 (20101)
  covalent geometry    : angle       0.63502 /  0.35 (28473)
  hydrogen bonds       : bond        0.04426 /  2.97 (  970)
  hydrogen bonds       : angle       3.88732 /  2.62 ( 2449)
  metal coordination   : bond        0.00592 /  0.34 (   16)
  metal coordination   : angle       4.44433 /  2.97 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2498.12 seconds
wall clock time: 44 minutes 13.09 seconds (2653.09 seconds total)