Starting phenix.real_space_refine
on Wed Mar  4 19:17:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zol_14847/03_2026/7zol_14847.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zol_14847/03_2026/7zol_14847.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zol_14847/03_2026/7zol_14847.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zol_14847/03_2026/7zol_14847.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zol_14847/03_2026/7zol_14847.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zol_14847/03_2026/7zol_14847.map"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.041
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      38      5.49       5
     S      52      5.16       5
     C    9648      2.51       5
     N    2736      2.21       5
     O    2962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15440
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 13412
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1702, 13403
          Classifications: {'peptide': 1702}
          Incomplete info: {'truncation_to_alanine': 119}
          Link IDs: {'PTRANS': 84, 'TRANS': 1617}
          Chain breaks: 7
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 436
          Unresolved non-hydrogen angles: 551
          Unresolved non-hydrogen dihedrals: 361
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 12, 'ARG:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 259
      Conformer: "B"
        Number of residues, atoms: 1702, 13403
          Classifications: {'peptide': 1702}
          Incomplete info: {'truncation_to_alanine': 119}
          Link IDs: {'PTRANS': 84, 'TRANS': 1617}
          Chain breaks: 7
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 436
          Unresolved non-hydrogen angles: 551
          Unresolved non-hydrogen dihedrals: 361
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 12, 'ARG:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 259
          bond proxies already assigned to first conformer: 13670
    Chain: "C"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 813
          Classifications: {'RNA': 39}
          Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 4, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 21, 'rna3p': 17}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 1211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1211
          Classifications: {'peptide': 150}
          Link IDs: {'PTRANS': 6, 'TRANS': 143}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7424  SG  CYS B 997      52.572  64.921  95.672  1.00 11.39           S
  ATOM  11124  SG  CYS B1515      55.183  64.566  98.350  1.00 11.39           S
  ATOM  11373  SG  CYS B1545      53.764  68.043  97.285  1.00 11.39           S
  ATOM  11391  SG  CYS B1548      51.704  65.738  99.370  1.00 32.20           S
  ATOM    679  SG  CYS B  97      36.980  36.901 188.081  1.00 29.10           S
  ATOM    954  SG  CYS B 131      36.283  33.384 189.576  1.00 42.45           S
  ATOM   1004  SG  CYS B 137      34.131  34.812 186.698  1.00 26.04           S
  ATOM   1028  SG  CYS B 140      37.685  33.867 186.068  1.00 19.90           S
  ATOM   3726  SG  CYS B 498      47.565  57.863 160.556  1.00 18.78           S
  ATOM   3803  SG  CYS B 508      48.651  56.011 163.614  1.00 32.36           S
  ATOM   3815  SG  CYS B 510      46.302  58.939 163.979  1.00 17.63           S
  ATOM   3835  SG  CYS B 513      45.053  55.676 162.419  1.00 11.39           S
  ATOM   5519  SG  CYS B 757      59.105  70.623 133.930  1.00 23.99           S
  ATOM   5531  SG  CYS B 759      55.824  72.415 133.124  1.00 11.39           S
  ATOM   5552  SG  CYS B 762      55.751  68.741 134.169  1.00 11.39           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ALYS B1526 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B1526 " occ=0.50
  Time building chain proxies: 5.17, per 1000 atoms: 0.33
  Number of scatterers: 15440
  At special positions: 0
  Unit cell: (94.4906, 105.983, 203.027, 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      52     16.00
     P      38     15.00
     O    2962      8.00
     N    2736      7.00
     C    9648      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 997.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1801 "
        pdb="ZN    ZN B1801 " - pdb=" SG  CYS B1545 "
        pdb="ZN    ZN B1801 " - pdb=" SG  CYS B 997 "
        pdb="ZN    ZN B1801 " - pdb=" SG  CYS B1548 "
        pdb="ZN    ZN B1801 " - pdb=" SG  CYS B1515 "
      pdb="  ZN B1802 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B 140 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B  97 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B 137 "
        pdb="ZN    ZN B1802 " - pdb=" SG  CYS B 131 "
      pdb="  ZN B1803 "
        pdb="ZN    ZN B1803 " - pdb=" SG  CYS B 508 "
        pdb="ZN    ZN B1803 " - pdb=" SG  CYS B 498 "
        pdb="ZN    ZN B1803 " - pdb=" SG  CYS B 510 "
        pdb="ZN    ZN B1803 " - pdb=" SG  CYS B 513 "
      pdb="  ZN B1804 "
        pdb="ZN    ZN B1804 " - pdb=" ND1 HIS B 754 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B 759 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B 757 "
        pdb="ZN    ZN B1804 " - pdb=" SG  CYS B 762 "
      Number of angles added : 21


  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3492

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 21 sheets defined
      34.7% alpha, 13.4% beta
      0 base pairs and 9 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 36 through 40
    Processing helix  chain 'B' and resid 42 through 47
    Processing helix  chain 'B' and resid 68 through 87
      removed outlier: 4.078A  pdb=" N   VAL B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 144
    Processing helix  chain 'B' and resid 145 through 148
      removed outlier: 3.801A  pdb=" N   LYS B 148 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 145 through 148'
    Processing helix  chain 'B' and resid 177 through 181
      removed outlier: 3.559A  pdb=" N   VAL B 181 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 245
    Processing helix  chain 'B' and resid 291 through 309
    Processing helix  chain 'B' and resid 311 through 313
      No H-bonds generated for 'chain 'B' and resid 311 through 313'
    Processing helix  chain 'B' and resid 314 through 329
      removed outlier: 4.264A  pdb=" N   ARG B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 377
      removed outlier: 3.530A  pdb=" N   PHE B 367 " --> pdb=" O   ARG B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 401
    Processing helix  chain 'B' and resid 478 through 495
      removed outlier: 3.540A  pdb=" N   LEU B 482 " --> pdb=" O   PRO B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 517
      removed outlier: 4.024A  pdb=" N   CYS B 513 " --> pdb=" O   SER B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 592
      removed outlier: 3.543A  pdb=" N   GLN B 591 " --> pdb=" O   SER B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 630
      removed outlier: 3.968A  pdb=" N   THR B 629 " --> pdb=" O   LYS B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 633
      No H-bonds generated for 'chain 'B' and resid 631 through 633'
    Processing helix  chain 'B' and resid 672 through 676
    Processing helix  chain 'B' and resid 731 through 748
    Processing helix  chain 'B' and resid 759 through 765
    Processing helix  chain 'B' and resid 834 through 851
    Processing helix  chain 'B' and resid 858 through 862
      removed outlier: 3.578A  pdb=" N   GLY B 862 " --> pdb=" O   GLY B 859 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 869 through 873
      removed outlier: 3.924A  pdb=" N   HIS B 873 " --> pdb=" O   PRO B 870 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 884 through 889
    Processing helix  chain 'B' and resid 978 through 995
      removed outlier: 4.184A  pdb=" N   ILE B 982 " --> pdb=" O   PRO B 978 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1058 through 1065
      removed outlier: 3.698A  pdb=" N   ASN B1062 " --> pdb=" O   ASN B1058 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1076 through 1084
      removed outlier: 3.720A  pdb=" N   GLU B1080 " --> pdb=" O   ASP B1076 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1088 through 1100
      Proline residue:  B1097  - end of helix
    Processing helix  chain 'B' and resid 1107 through 1120
    Processing helix  chain 'B' and resid 1125 through 1133
      removed outlier: 3.543A  pdb=" N   ILE B1129 " --> pdb=" O   ASN B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1141 through 1147
      removed outlier: 3.857A  pdb=" N   LEU B1145 " --> pdb=" O   THR B1141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1155 through 1165
      removed outlier: 4.021A  pdb=" N   LEU B1165 " --> pdb=" O   GLN B1161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1172 through 1184
      removed outlier: 3.507A  pdb=" N   VAL B1184 " --> pdb=" O   LEU B1180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1189 through 1196
      removed outlier: 3.506A  pdb=" N   LEU B1196 " --> pdb=" O   ILE B1192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1197 through 1199
      No H-bonds generated for 'chain 'B' and resid 1197 through 1199'
    Processing helix  chain 'B' and resid 1206 through 1216
    Processing helix  chain 'B' and resid 1219 through 1229
      removed outlier: 3.796A  pdb=" N   VAL B1223 " --> pdb=" O   PRO B1219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1237 through 1259
      removed outlier: 3.774A  pdb=" N   HIS B1259 " --> pdb=" O   LEU B1255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1274 through 1283
      removed outlier: 3.584A  pdb=" N   LEU B1283 " --> pdb=" O   MET B1279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1431 through 1452
      removed outlier: 3.900A  pdb=" N   GLU B1435 " --> pdb=" O   PRO B1431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1500 through 1504
    Processing helix  chain 'B' and resid 1518 through 1522
      removed outlier: 3.952A  pdb=" N   ASP B1521 " --> pdb=" O   GLU B1518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1524 through 1532
    Processing helix  chain 'B' and resid 1545 through 1552
    Processing helix  chain 'B' and resid 1574 through 1579
      removed outlier: 3.883A  pdb=" N   ASN B1577 " --> pdb=" O   LEU B1574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1613 through 1621
    Processing helix  chain 'B' and resid 1659 through 1671
    Processing helix  chain 'B' and resid 1683 through 1687
    Processing helix  chain 'B' and resid 1706 through 1723
    Processing helix  chain 'B' and resid 1726 through 1736
    Processing helix  chain 'B' and resid 1763 through 1771
      removed outlier: 3.606A  pdb=" N   GLU B1770 " --> pdb=" O   GLU B1766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 33
      removed outlier: 3.549A  pdb=" N   LEU A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 79
      removed outlier: 4.209A  pdb=" N   LYS A  66 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU A  67 " --> pdb=" O   GLN A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 114
      removed outlier: 3.608A  pdb=" N   LYS A 100 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 119
    Processing helix  chain 'A' and resid 123 through 151
      removed outlier: 3.553A  pdb=" N   ILE A 150 " --> pdb=" O   HIS A 146 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 67
    Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30
      removed outlier: 3.521A  pdb=" N   PHE B  29 " --> pdb=" O   ILE B 206 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ARG B 189 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL B 187 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   ASN B 202 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ARG B 185 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   TRP B 204 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ASP B 183 " --> pdb=" O   TRP B 204 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 123
      removed outlier: 5.736A  pdb=" N   THR B 122 " --> pdb=" O   ALA B 429 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 521
      removed outlier: 4.823A  pdb=" N   GLU B 442 " --> pdb=" O   ASN B 611 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ASN B 611 " --> pdb=" O   GLU B 442 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   VAL B 444 " --> pdb=" O   LEU B 609 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LEU B 609 " --> pdb=" O   VAL B 444 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453
      removed outlier: 3.979A  pdb=" N   LYS B 466 " --> pdb=" O   TRP B 453 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 477
      removed outlier: 3.774A  pdb=" N   SER B 524 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 538
    Processing sheet with id=AA9, first strand: chain 'B' and resid 653 through 662
      removed outlier: 4.828A  pdb=" N   LYS B 822 " --> pdb=" O   GLN B 782 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   TYR B 728 " --> pdb=" O   ILE B 781 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE B 727 " --> pdb=" O   THR B 688 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 653 through 662
    Processing sheet with id=AB2, first strand: chain 'B' and resid 790 through 792
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1745 through 1746
      removed outlier: 4.781A  pdb=" N   LYS B1745 " --> pdb=" O   LYS B 902 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY B1789 " --> pdb=" O   ILE B 903 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 907 through 910
    Processing sheet with id=AB5, first strand: chain 'B' and resid 976 through 977
    Processing sheet with id=AB6, first strand: chain 'B' and resid 976 through 977
      removed outlier: 5.830A  pdb=" N   TYR B 937 " --> pdb=" O   ASN B1657 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLU B1697 " --> pdb=" O   VAL B 942 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   THR B 944 " --> pdb=" O   VAL B1695 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   VAL B1695 " --> pdb=" O   THR B 944 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   GLU B 946 " --> pdb=" O   ILE B1693 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   ILE B1693 " --> pdb=" O   GLU B 946 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 954 through 959
      removed outlier: 6.747A  pdb=" N   GLU B 957 " --> pdb=" O   ASP B 967 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP B 967 " --> pdb=" O   GLU B 957 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER B 965 " --> pdb=" O   GLN B 959 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 1027 through 1029
      removed outlier: 3.723A  pdb=" N   ARG B1476 " --> pdb=" O   ASP B1486 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ASP B1486 " --> pdb=" O   ARG B1476 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 1044 through 1047
    Processing sheet with id=AC1, first strand: chain 'B' and resid 1169 through 1170
      removed outlier: 3.633A  pdb=" N   VAL B1138 " --> pdb=" O   TYR B1170 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   ARG B1135 " --> pdb=" O   ARG B1204 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ARG B1204 " --> pdb=" O   ARG B1135 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LYS B1137 " --> pdb=" O   ASP B1202 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG B1139 " --> pdb=" O   ASP B1200 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ASP B1200 " --> pdb=" O   ARG B1139 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 1378 through 1379
    Processing sheet with id=AC3, first strand: chain 'B' and resid 1581 through 1583
      removed outlier: 4.343A  pdb=" N   ARG B1638 " --> pdb=" O   LEU B1583 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1485 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      9 stacking parallelities
  Total time for adding SS restraints: 2.97

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4452
        1.33 -     1.46: 2894
        1.46 -     1.58: 8330
        1.58 -     1.70: 73
        1.70 -     1.82: 75
  Bond restraints: 15824
  Sorted by residual:
  bond pdb=" O3'   G C  11 "
       pdb=" P     A C  12 "
    ideal  model  delta    sigma   weight residual
    1.607  1.566  0.041 1.50e-02 4.44e+03 7.42e+00
  bond pdb=" O3'   A C  25 "
       pdb=" P     A C  26 "
    ideal  model  delta    sigma   weight residual
    1.607  1.569  0.038 1.50e-02 4.44e+03 6.34e+00
  bond pdb=" O3'   U C  24 "
       pdb=" P     A C  25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.577  0.030 1.50e-02 4.44e+03 4.10e+00
  bond pdb=" CA  LEU B1520 "
       pdb=" C   LEU B1520 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.34e-02 5.57e+03 3.96e+00
  bond pdb=" O3'   U C  27 "
       pdb=" P     U C  28 "
    ideal  model  delta    sigma   weight residual
    1.607  1.578  0.029 1.50e-02 4.44e+03 3.85e+00
  ... (remaining 15819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 21042
        1.90 -     3.81: 401
        3.81 -     5.71: 54
        5.71 -     7.62: 19
        7.62 -     9.52: 9
  Bond angle restraints: 21525
  Sorted by residual:
  angle pdb=" N   PRO B 289 "
        pdb=" CA  PRO B 289 "
        pdb=" CB  PRO B 289 "
      ideal   model   delta    sigma   weight residual
     103.08  111.52   -8.44 9.70e-01 1.06e+00 7.57e+01
  angle pdb=" N   PRO B1049 "
        pdb=" CA  PRO B1049 "
        pdb=" CB  PRO B1049 "
      ideal   model   delta    sigma   weight residual
     103.25  111.77   -8.52 1.05e+00 9.07e-01 6.58e+01
  angle pdb=" N   PRO B 277 "
        pdb=" CA  PRO B 277 "
        pdb=" CB  PRO B 277 "
      ideal   model   delta    sigma   weight residual
     101.88  109.98   -8.10 1.01e+00 9.80e-01 6.43e+01
  angle pdb=" N   PRO B1356 "
        pdb=" CA  PRO B1356 "
        pdb=" CB  PRO B1356 "
      ideal   model   delta    sigma   weight residual
     103.25  111.65   -8.40 1.05e+00 9.07e-01 6.41e+01
  angle pdb=" N   PRO B1031 "
        pdb=" CA  PRO B1031 "
        pdb=" CB  PRO B1031 "
      ideal   model   delta    sigma   weight residual
     103.25  111.48   -8.23 1.05e+00 9.07e-01 6.14e+01
  ... (remaining 21520 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.71: 9421
       35.71 -    71.42: 266
       71.42 -   107.13: 22
      107.13 -   142.84: 2
      142.84 -   178.56: 8
  Dihedral angle restraints: 9719
    sinusoidal: 4340
      harmonic: 5379
  Sorted by residual:
  dihedral pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
           pdb=" N1    U C   9 "
           pdb=" C2    U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   21.44  178.56     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U C  16 "
           pdb=" C1'   U C  16 "
           pdb=" N1    U C  16 "
           pdb=" C2    U C  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   29.08  170.92     1      1.50e+01 4.44e-03 8.48e+01
  dihedral pdb=" O4'   U C  24 "
           pdb=" C1'   U C  24 "
           pdb=" N1    U C  24 "
           pdb=" C2    U C  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.74  163.26     1      1.50e+01 4.44e-03 8.35e+01
  ... (remaining 9716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 2153
       0.078 -    0.156: 209
       0.156 -    0.234: 20
       0.234 -    0.312: 2
       0.312 -    0.389: 2
  Chirality restraints: 2386
  Sorted by residual:
  chirality pdb=" C1'   C C  15 "
            pdb=" O4'   C C  15 "
            pdb=" C2'   C C  15 "
            pdb=" N1    C C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.06    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" C1'   U C  27 "
            pdb=" O4'   U C  27 "
            pdb=" C2'   U C  27 "
            pdb=" N1    U C  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.12    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  PRO B1345 "
            pdb=" N   PRO B1345 "
            pdb=" C   PRO B1345 "
            pdb=" CB  PRO B1345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 2383 not shown)

  Planarity restraints: 2643
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B1468 "    0.057 5.00e-02 4.00e+02   8.83e-02 1.25e+01
        pdb=" N   PRO B1469 "   -0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO B1469 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B1469 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 345 "    0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO B 346 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 346 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 346 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 816 "    0.040 5.00e-02 4.00e+02   6.12e-02 6.00e+00
        pdb=" N   PRO B 817 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B 817 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 817 "    0.034 5.00e-02 4.00e+02
  ... (remaining 2640 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1814
        2.75 -     3.29: 14328
        3.29 -     3.83: 23569
        3.83 -     4.36: 28037
        4.36 -     4.90: 48551
  Nonbonded interactions: 116299
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 923 "
            pdb=" OH  TYR B1556 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE2 GLU B 935 "
            pdb=" NZ  LYS B1703 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OD1 ASN A  78 "
            pdb=" NH2 ARG A  81 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   LEU B 317 "
            pdb=" OG1 THR B 321 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   LYS B1449 "
            pdb=" NZ  LYS B1452 "
     model   vdw
     2.308 3.120
  ... (remaining 116294 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.230
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
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      :  0.003   0.041  15840  Z= 0.144
  Angle     :  0.646   9.524  21546  Z= 0.382
  Chirality :  0.047   0.389   2386
  Planarity :  0.005   0.088   2643
  Dihedral  : 17.391 178.556   6227
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  6.54 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.26 %
    Favored  : 99.54 %
  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: -0.47 (0.20), residues: 1837
  helix:  1.48 (0.22), residues: 593
  sheet:  0.81 (0.38), residues: 202
  loop : -1.73 (0.18), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1588 
 TYR   0.018   0.001   TYR B1444 
 PHE   0.009   0.001   PHE B 808 
 TRP   0.009   0.001   TRP B1788 
 HIS   0.002   0.001   HIS B 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (15824)
  covalent geometry    : angle       0.64189 (21525)
  hydrogen bonds       : bond        0.21720 (  514)
  hydrogen bonds       : angle       6.55994 ( 1485)
  metal coordination   : bond        0.00488 (   16)
  metal coordination   : angle       2.28087 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.630 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1234
  time to fit residues: 23.1728
Evaluate side-chains
  94 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 159 ASN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1126 GLN
** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.182726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130169 restraints weight = 42122.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 3.93
r_work: 0.3478 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  15840  Z= 0.280
  Angle     :  0.815  12.471  21546  Z= 0.413
  Chirality :  0.052   0.500   2386
  Planarity :  0.007   0.077   2643
  Dihedral  : 16.417 179.572   2600
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  7.74 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  6.36 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.19), residues: 1837
  helix:  0.94 (0.22), residues: 589
  sheet:  0.11 (0.37), residues: 198
  loop : -2.05 (0.17), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 983 
 TYR   0.017   0.002   TYR B 868 
 PHE   0.030   0.003   PHE B 855 
 TRP   0.017   0.002   TRP B1788 
 HIS   0.007   0.002   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (15824)
  covalent geometry    : angle       0.81011 (21525)
  hydrogen bonds       : bond        0.06001 (  514)
  hydrogen bonds       : angle       5.17905 ( 1485)
  metal coordination   : bond        0.01380 (   16)
  metal coordination   : angle       2.85012 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: B  178 ILE cc_start: 0.8870 (tp) cc_final: 0.8662 (tp)
REVERT: B  829 ILE cc_start: 0.8587 (pt) cc_final: 0.8369 (mt)
REVERT: B  831 ARG cc_start: 0.7871 (ptt90) cc_final: 0.7526 (ptt180)
REVERT: B  901 ASP cc_start: 0.8215 (t0) cc_final: 0.7965 (t0)
REVERT: B 1715 MET cc_start: 0.8560 (mmm) cc_final: 0.8330 (tpt)
REVERT: A   28 LEU cc_start: 0.7878 (mt) cc_final: 0.7628 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1186
  time to fit residues: 21.3780
Evaluate side-chains
  100 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1279 MET
Chi-restraints excluded: chain B residue 1379 ILE
Chi-restraints excluded: chain A residue   23 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 118 optimal weight:    8.9990
   chunk 153 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 168 optimal weight:    0.1980
   chunk 149 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1445 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.187667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135719 restraints weight = 47444.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 3.71
r_work: 0.3563 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15840  Z= 0.112
  Angle     :  0.600  10.396  21546  Z= 0.302
  Chirality :  0.043   0.287   2386
  Planarity :  0.005   0.065   2643
  Dihedral  : 16.059 179.457   2600
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  6.32 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.66 %
    Favored  : 90.49 %
  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: -0.71 (0.19), residues: 1837
  helix:  1.45 (0.22), residues: 591
  sheet:  0.36 (0.37), residues: 205
  loop : -1.92 (0.17), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 326 
 TYR   0.010   0.001   TYR B1772 
 PHE   0.012   0.001   PHE B1475 
 TRP   0.011   0.001   TRP B1788 
 HIS   0.002   0.001   HIS B1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (15824)
  covalent geometry    : angle       0.59705 (21525)
  hydrogen bonds       : bond        0.04055 (  514)
  hydrogen bonds       : angle       4.55004 ( 1485)
  metal coordination   : bond        0.00442 (   16)
  metal coordination   : angle       2.10499 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: B  199 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7589 (p0)
REVERT: B  516 MET cc_start: 0.8469 (mmm) cc_final: 0.8079 (mmm)
REVERT: B  871 LEU cc_start: 0.7672 (mp) cc_final: 0.7466 (mt)
REVERT: B  901 ASP cc_start: 0.8167 (t0) cc_final: 0.7872 (t0)
REVERT: B 1239 LYS cc_start: 0.4473 (OUTLIER) cc_final: 0.3919 (pttp)
REVERT: B 1409 TYR cc_start: 0.5196 (m-10) cc_final: 0.4698 (m-10)
REVERT: B 1520 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5178 (mt)
REVERT: B 1715 MET cc_start: 0.8501 (mmm) cc_final: 0.8245 (tpt)
REVERT: B 1769 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8058 (mmmt)
  outliers start: 11
  outliers final: 7
  residues processed: 108
  average time/residue: 0.1195
  time to fit residues: 20.1024
Evaluate side-chains
  104 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1239 LYS
Chi-restraints excluded: chain B residue 1279 MET
Chi-restraints excluded: chain B residue 1520 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 111 optimal weight:    0.0970
   chunk 7 optimal weight:    8.9990
   chunk 159 optimal weight:    0.2980
   chunk 54 optimal weight:    7.9990
   chunk 65 optimal weight:    0.4980
   chunk 160 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1271 ASN ** 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 = 0.4307 r_free = 0.4307 target = 0.187940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136185 restraints weight = 44572.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 3.60
r_work: 0.3571 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15840  Z= 0.110
  Angle     :  0.588  11.297  21546  Z= 0.293
  Chirality :  0.043   0.293   2386
  Planarity :  0.005   0.063   2643
  Dihedral  : 15.964 179.523   2600
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  6.60 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.32 %
    Favored  : 89.57 %
  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: -0.55 (0.19), residues: 1837
  helix:  1.62 (0.22), residues: 598
  sheet:  0.47 (0.37), residues: 204
  loop : -1.88 (0.17), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 326 
 TYR   0.010   0.001   TYR B1409 
 PHE   0.009   0.001   PHE B 806 
 TRP   0.014   0.001   TRP B 437 
 HIS   0.002   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (15824)
  covalent geometry    : angle       0.58336 (21525)
  hydrogen bonds       : bond        0.03707 (  514)
  hydrogen bonds       : angle       4.33440 ( 1485)
  metal coordination   : bond        0.00412 (   16)
  metal coordination   : angle       2.34732 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: B  102 ASN cc_start: 0.7605 (t0) cc_final: 0.7381 (t0)
REVERT: B  199 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7509 (p0)
REVERT: B  334 ASP cc_start: 0.8555 (t70) cc_final: 0.8326 (t0)
REVERT: B  829 ILE cc_start: 0.8629 (pt) cc_final: 0.8319 (mt)
REVERT: B  871 LEU cc_start: 0.7699 (mp) cc_final: 0.7461 (mt)
REVERT: B  901 ASP cc_start: 0.8180 (t0) cc_final: 0.7914 (t0)
REVERT: B 1109 GLU cc_start: 0.5974 (mp0) cc_final: 0.5655 (tt0)
REVERT: B 1409 TYR cc_start: 0.5443 (m-10) cc_final: 0.4938 (m-10)
REVERT: B 1520 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.5179 (mt)
REVERT: B 1715 MET cc_start: 0.8537 (mmm) cc_final: 0.8278 (tpt)
REVERT: B 1761 GLU cc_start: 0.5940 (tt0) cc_final: 0.5729 (tt0)
REVERT: B 1769 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7953 (mmmt)
REVERT: A   35 GLU cc_start: 0.7557 (pm20) cc_final: 0.7224 (pm20)
REVERT: A   63 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7304 (tp40)
  outliers start: 15
  outliers final: 9
  residues processed: 112
  average time/residue: 0.1112
  time to fit residues: 19.7463
Evaluate side-chains
  111 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  985 MET
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1520 LEU
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 140 optimal weight:    4.9990
   chunk 166 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 176 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 181 optimal weight:    0.6980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
B1198 ASN
** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1580 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.182864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.130721 restraints weight = 43386.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 3.49
r_work: 0.3511 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3515
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3515 r_free = 0.3515    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3515 r_free = 0.3515    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3515
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  15840  Z= 0.212
  Angle     :  0.704  11.334  21546  Z= 0.354
  Chirality :  0.048   0.415   2386
  Planarity :  0.006   0.058   2643
  Dihedral  : 16.250 178.961   2600
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.85 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.83 %
    Favored  : 87.93 %
  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: -0.87 (0.19), residues: 1837
  helix:  1.35 (0.22), residues: 591
  sheet:  0.17 (0.37), residues: 198
  loop : -2.00 (0.17), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 145 
 TYR   0.014   0.002   TYR B 435 
 PHE   0.020   0.002   PHE B 735 
 TRP   0.018   0.002   TRP B1788 
 HIS   0.005   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (15824)
  covalent geometry    : angle       0.69918 (21525)
  hydrogen bonds       : bond        0.04903 (  514)
  hydrogen bonds       : angle       4.65410 ( 1485)
  metal coordination   : bond        0.00871 (   16)
  metal coordination   : angle       2.67709 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.409 
Fit side-chains
REVERT: B  325 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7404 (mt)
REVERT: B  871 LEU cc_start: 0.7872 (mp) cc_final: 0.7666 (mt)
REVERT: B  901 ASP cc_start: 0.8198 (t0) cc_final: 0.7924 (t0)
REVERT: B 1109 GLU cc_start: 0.6101 (mp0) cc_final: 0.5672 (tt0)
REVERT: B 1409 TYR cc_start: 0.5652 (m-10) cc_final: 0.4921 (m-10)
REVERT: B 1769 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8164 (mmmt)
REVERT: A   63 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6881 (tp40)
  outliers start: 17
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1183
  time to fit residues: 18.4467
Evaluate side-chains
  101 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 143 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 58 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 170 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 165 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B1220 GLN
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.186530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134455 restraints weight = 48398.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.73
r_work: 0.3546 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15840  Z= 0.114
  Angle     :  0.604  12.331  21546  Z= 0.298
  Chirality :  0.043   0.284   2386
  Planarity :  0.005   0.058   2643
  Dihedral  : 15.977 179.083   2600
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  6.87 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.68 %
    Favored  : 87.20 %
  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: -0.64 (0.20), residues: 1837
  helix:  1.58 (0.22), residues: 598
  sheet:  0.37 (0.36), residues: 213
  loop : -1.96 (0.18), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 326 
 TYR   0.010   0.001   TYR B1409 
 PHE   0.009   0.001   PHE B 350 
 TRP   0.011   0.001   TRP B1788 
 HIS   0.003   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (15824)
  covalent geometry    : angle       0.59941 (21525)
  hydrogen bonds       : bond        0.03565 (  514)
  hydrogen bonds       : angle       4.31568 ( 1485)
  metal coordination   : bond        0.00455 (   16)
  metal coordination   : angle       2.32687 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: B  102 ASN cc_start: 0.7591 (t0) cc_final: 0.7318 (t0)
REVERT: B  199 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7563 (p0)
REVERT: B  325 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7374 (mt)
REVERT: B  516 MET cc_start: 0.8421 (mmm) cc_final: 0.8180 (mmm)
REVERT: B  813 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8263 (mp)
REVERT: B  829 ILE cc_start: 0.8577 (pt) cc_final: 0.8303 (mt)
REVERT: B  901 ASP cc_start: 0.8263 (t0) cc_final: 0.7997 (t0)
REVERT: B 1409 TYR cc_start: 0.5592 (m-10) cc_final: 0.4846 (m-10)
REVERT: B 1769 LYS cc_start: 0.8288 (mmtp) cc_final: 0.8081 (mmmt)
REVERT: A   63 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7207 (tp40)
  outliers start: 15
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1212
  time to fit residues: 20.8002
Evaluate side-chains
  108 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  813 ILE
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1279 MET
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 157 optimal weight:    5.9990
   chunk 170 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 181 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 122 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 131 optimal weight:    8.9990
   chunk 105 optimal weight:    7.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 446 GLN
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.179487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.126976 restraints weight = 52450.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 4.41
r_work: 0.3421 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3425
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.072  15840  Z= 0.350
  Angle     :  0.847  12.838  21546  Z= 0.426
  Chirality :  0.054   0.495   2386
  Planarity :  0.007   0.066   2643
  Dihedral  : 16.398 179.864   2600
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  9.00 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.94 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.19), residues: 1837
  helix:  0.97 (0.22), residues: 590
  sheet:  0.24 (0.36), residues: 208
  loop : -2.32 (0.17), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 983 
 TYR   0.019   0.003   TYR B 435 
 PHE   0.025   0.003   PHE B1419 
 TRP   0.019   0.003   TRP B 437 
 HIS   0.009   0.002   HIS B1611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00848 (15824)
  covalent geometry    : angle       0.84112 (21525)
  hydrogen bonds       : bond        0.05886 (  514)
  hydrogen bonds       : angle       4.93236 ( 1485)
  metal coordination   : bond        0.01227 (   16)
  metal coordination   : angle       3.27360 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.638 
Fit side-chains
REVERT: B  325 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7540 (mt)
REVERT: B  431 GLN cc_start: 0.7569 (tp-100) cc_final: 0.6707 (pp30)
REVERT: B  807 LYS cc_start: 0.6784 (tmtt) cc_final: 0.6568 (tmtt)
REVERT: B  813 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8348 (mp)
REVERT: B  901 ASP cc_start: 0.8314 (t0) cc_final: 0.8016 (t0)
REVERT: B 1109 GLU cc_start: 0.6117 (mp0) cc_final: 0.5781 (tt0)
REVERT: A   63 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6922 (tp40)
  outliers start: 22
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1202
  time to fit residues: 19.7258
Evaluate side-chains
  104 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  329 ASP
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  657 THR
Chi-restraints excluded: chain B residue  813 ILE
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1453 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 187 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 170 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 154 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 114 optimal weight:   10.0000
   chunk 179 optimal weight:   10.0000
   chunk 177 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 446 GLN
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.184547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.133190 restraints weight = 48891.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 4.40
r_work: 0.3492 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15840  Z= 0.126
  Angle     :  0.632  12.366  21546  Z= 0.315
  Chirality :  0.044   0.305   2386
  Planarity :  0.005   0.061   2643
  Dihedral  : 16.067 179.182   2600
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  6.76 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.53 %
    Favored  : 86.02 %
  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: -0.91 (0.19), residues: 1837
  helix:  1.41 (0.23), residues: 593
  sheet:  0.01 (0.36), residues: 215
  loop : -2.10 (0.18), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 983 
 TYR   0.011   0.001   TYR B1409 
 PHE   0.024   0.001   PHE B1475 
 TRP   0.012   0.001   TRP B 437 
 HIS   0.003   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (15824)
  covalent geometry    : angle       0.62769 (21525)
  hydrogen bonds       : bond        0.03773 (  514)
  hydrogen bonds       : angle       4.44717 ( 1485)
  metal coordination   : bond        0.00543 (   16)
  metal coordination   : angle       2.45439 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.669 
Fit side-chains
REVERT: B  199 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7160 (p0)
REVERT: B  325 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7435 (mt)
REVERT: B  550 LYS cc_start: 0.8107 (tppt) cc_final: 0.7856 (tppt)
REVERT: B  813 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: B  901 ASP cc_start: 0.8319 (t0) cc_final: 0.8025 (t0)
REVERT: A   63 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6990 (tp40)
  outliers start: 20
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1317
  time to fit residues: 21.9787
Evaluate side-chains
  111 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  657 THR
Chi-restraints excluded: chain B residue  813 ILE
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1290 HIS
Chi-restraints excluded: chain B residue 1453 THR
Chi-restraints excluded: chain B residue 1560 ILE
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 113 optimal weight:   20.0000
   chunk 98 optimal weight:    0.5980
   chunk 146 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 150 optimal weight:    0.8980
   chunk 132 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 177 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1372 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.183620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.131222 restraints weight = 48405.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 3.72
r_work: 0.3505 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15840  Z= 0.154
  Angle     :  0.651  12.068  21546  Z= 0.325
  Chirality :  0.045   0.353   2386
  Planarity :  0.005   0.059   2643
  Dihedral  : 16.073 179.554   2600
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.96 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.73 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.20), residues: 1837
  helix:  1.48 (0.22), residues: 591
  sheet:  0.04 (0.36), residues: 215
  loop : -2.10 (0.18), residues: 1031

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 145 
 TYR   0.012   0.001   TYR B1409 
 PHE   0.017   0.001   PHE B1475 
 TRP   0.016   0.001   TRP B 437 
 HIS   0.005   0.001   HIS B1290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (15824)
  covalent geometry    : angle       0.64655 (21525)
  hydrogen bonds       : bond        0.04058 (  514)
  hydrogen bonds       : angle       4.46621 ( 1485)
  metal coordination   : bond        0.00617 (   16)
  metal coordination   : angle       2.57615 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.565 
Fit side-chains
REVERT: B  325 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7409 (mt)
REVERT: B  550 LYS cc_start: 0.8090 (tppt) cc_final: 0.7838 (tppt)
REVERT: B  813 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8283 (mp)
REVERT: B  901 ASP cc_start: 0.8301 (t0) cc_final: 0.8023 (t0)
REVERT: A   63 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7036 (tp40)
  outliers start: 18
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1100
  time to fit residues: 18.2218
Evaluate side-chains
  111 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  657 THR
Chi-restraints excluded: chain B residue  813 ILE
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1290 HIS
Chi-restraints excluded: chain B residue 1372 ASN
Chi-restraints excluded: chain B residue 1453 THR
Chi-restraints excluded: chain B residue 1560 ILE
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 147 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 122 optimal weight:    8.9990
   chunk 68 optimal weight:    0.1980
   chunk 55 optimal weight:    3.9990
   chunk 136 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 161 optimal weight:    2.9990
   chunk 105 optimal weight:   20.0000
   chunk 18 optimal weight:    2.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1372 ASN
** A  39 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 = 0.4264 r_free = 0.4264 target = 0.183594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.132673 restraints weight = 37668.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 3.85
r_work: 0.3508 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3518
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3518
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.146  15840  Z= 0.192
  Angle     :  0.844  59.199  21546  Z= 0.467
  Chirality :  0.046   0.510   2386
  Planarity :  0.005   0.059   2643
  Dihedral  : 16.076 179.552   2600
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.85 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.66 %
    Favored  : 85.89 %
  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: -0.87 (0.20), residues: 1837
  helix:  1.48 (0.22), residues: 591
  sheet:  0.04 (0.36), residues: 215
  loop : -2.10 (0.18), residues: 1031

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 145 
 TYR   0.011   0.001   TYR B1409 
 PHE   0.015   0.001   PHE B1475 
 TRP   0.015   0.001   TRP B 437 
 HIS   0.005   0.001   HIS B1290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (15824)
  covalent geometry    : angle       0.84046 (21525)
  hydrogen bonds       : bond        0.04044 (  514)
  hydrogen bonds       : angle       4.46575 ( 1485)
  metal coordination   : bond        0.00596 (   16)
  metal coordination   : angle       2.57593 (   21)

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

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

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3674 Ramachandran restraints generated.
    1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.452 
Fit side-chains
REVERT: B  325 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7364 (mt)
REVERT: B  550 LYS cc_start: 0.8080 (tppt) cc_final: 0.7830 (tppt)
REVERT: B  813 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: B  901 ASP cc_start: 0.8300 (t0) cc_final: 0.8008 (t0)
REVERT: A   63 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7046 (tp40)
  outliers start: 20
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1195
  time to fit residues: 19.3263
Evaluate side-chains
  112 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  657 THR
Chi-restraints excluded: chain B residue  793 VAL
Chi-restraints excluded: chain B residue  813 ILE
Chi-restraints excluded: chain B residue  991 GLU
Chi-restraints excluded: chain B residue 1290 HIS
Chi-restraints excluded: chain B residue 1453 THR
Chi-restraints excluded: chain B residue 1560 ILE
Chi-restraints excluded: chain B residue 1715 MET
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 184 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 149 optimal weight:    1.9990
   chunk 114 optimal weight:   10.0000
   chunk 128 optimal weight:   50.0000
   chunk 105 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 166 optimal weight:    4.9990
   chunk 107 optimal weight:   20.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 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 = 0.4264 r_free = 0.4264 target = 0.183602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131145 restraints weight = 49482.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 3.76
r_work: 0.3503 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.146  15840  Z= 0.192
  Angle     :  0.844  59.199  21546  Z= 0.467
  Chirality :  0.046   0.510   2386
  Planarity :  0.005   0.059   2643
  Dihedral  : 16.076 179.552   2600
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.85 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.73 %
    Favored  : 85.89 %
  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: -0.87 (0.20), residues: 1837
  helix:  1.48 (0.22), residues: 591
  sheet:  0.04 (0.36), residues: 215
  loop : -2.10 (0.18), residues: 1031

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 145 
 TYR   0.011   0.001   TYR B1409 
 PHE   0.015   0.001   PHE B1475 
 TRP   0.015   0.001   TRP B 437 
 HIS   0.005   0.001   HIS B1290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (15824)
  covalent geometry    : angle       0.84046 (21525)
  hydrogen bonds       : bond        0.04044 (  514)
  hydrogen bonds       : angle       4.46575 ( 1485)
  metal coordination   : bond        0.00596 (   16)
  metal coordination   : angle       2.57593 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4490.46 seconds
wall clock time: 77 minutes 11.19 seconds (4631.19 seconds total)