Starting phenix.real_space_refine
on Thu Sep 18 09:50:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qaz_52980/09_2025/9qaz_52980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qaz_52980/09_2025/9qaz_52980.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qaz_52980/09_2025/9qaz_52980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qaz_52980/09_2025/9qaz_52980.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qaz_52980/09_2025/9qaz_52980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qaz_52980/09_2025/9qaz_52980.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     260      5.49       5
     S      42      5.16       5
     C    8819      2.51       5
     N    2812      2.21       5
     O    3538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15471
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 954, 7649
          Classifications: {'peptide': 954}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 55, 'TRANS': 895}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 5371
          Classifications: {'RNA': 253}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 18, 'rna3p_pur': 99, 'rna3p_pyr': 119}
          Link IDs: {'rna2p': 35, 'rna3p': 217}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 632
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
    Chain: "M"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "N"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 149
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "O"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 971
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
          Chain breaks: 3
  Time building chain proxies: 3.89, per 1000 atoms: 0.25
  Number of scatterers: 15471
  At special positions: 0
  Unit cell: (167.322, 123.903, 145.083, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P     260     15.00
     O    3538      8.00
     N    2812      7.00
     C    8819      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: 1.23
  Conformation dependent library (CDL) restraints added in 538.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2346

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 9 sheets defined
      54.1% alpha, 12.7% beta
      71 base pairs and 125 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
      removed outlier: 3.898A  pdb=" N   ARG A  11 " --> pdb=" O   CYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 18
      No H-bonds generated for 'chain 'A' and resid 16 through 18'
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 3.587A  pdb=" N   VAL A  51 " --> pdb=" O   PHE A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 92
      removed outlier: 3.580A  pdb=" N   VAL A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLU A  90 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
      removed outlier: 3.847A  pdb=" N   GLY A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.797A  pdb=" N   ARG A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.737A  pdb=" N   LEU A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 3.648A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.504A  pdb=" N   LEU A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A 410 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 454
      removed outlier: 3.507A  pdb=" N   ARG A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 473
      removed outlier: 3.910A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.707A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 497
      removed outlier: 3.504A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.684A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
      removed outlier: 3.525A  pdb=" N   LYS A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
      removed outlier: 3.627A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 597
      removed outlier: 3.713A  pdb=" N   LYS A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.664A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 4.081A  pdb=" N   LYS A 659 " --> pdb=" O   THR A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.832A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 734
      removed outlier: 3.653A  pdb=" N   GLU A 727 " --> pdb=" O   ASP A 723 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE A 733 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.575A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 814
    Processing helix  chain 'A' and resid 837 through 854
      removed outlier: 3.661A  pdb=" N   CYS A 842 " --> pdb=" O   SER A 838 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS A 852 " --> pdb=" O   ASP A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 859
    Processing helix  chain 'A' and resid 876 through 890
      removed outlier: 3.680A  pdb=" N   ALA A 880 " --> pdb=" O   HIS A 876 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY A 890 " --> pdb=" O   THR A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.602A  pdb=" N   TYR A 949 " --> pdb=" O   TYR A 946 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 946 through 950'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.547A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
      removed outlier: 3.546A  pdb=" N   LEU A1007 " --> pdb=" O   LYS A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1028
      removed outlier: 3.541A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1051
      removed outlier: 3.552A  pdb=" N   ASP A1038 " --> pdb=" O   ARG A1034 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   CYS A1043 " --> pdb=" O   THR A1039 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1085
      removed outlier: 3.898A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   HIS A1075 " --> pdb=" O   GLN A1071 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   THR A1083 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ARG A1084 " --> pdb=" O   LEU A1080 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   HIS A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.606A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.091A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLN A1102 " --> pdb=" O   THR A1098 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.875A  pdb=" N   THR A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 38
      removed outlier: 4.400A  pdb=" N   LEU L  34 " --> pdb=" O   ARG L  30 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY L  38 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 48 through 73
      removed outlier: 3.600A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   THR L  60 " --> pdb=" O   LEU L  56 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE L  63 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 91
      removed outlier: 3.961A  pdb=" N   LEU L  84 " --> pdb=" O   ILE L  80 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP L  91 " --> pdb=" O   ALA L  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 91 through 99
      removed outlier: 3.635A  pdb=" N   ASN L  95 " --> pdb=" O   ASP L  91 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LYS L  96 " --> pdb=" O   GLU L  92 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 40 through 50
      removed outlier: 3.627A  pdb=" N   VAL M  45 " --> pdb=" O   TYR M  41 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS M  47 " --> pdb=" O   TYR M  43 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 3.995A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER M  79 " --> pdb=" O   ALA M  75 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   HIS M  83 " --> pdb=" O   SER M  79 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TYR M  84 " --> pdb=" O   ARG M  80 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 3.782A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU M 103 " --> pdb=" O   VAL M  99 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 107 through 125
      removed outlier: 3.757A  pdb=" N   SER M 113 " --> pdb=" O   LYS M 109 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU M 114 " --> pdb=" O   HIS M 110 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY M 115 " --> pdb=" O   ALA M 111 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR M 120 " --> pdb=" O   THR M 116 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER M 125 " --> pdb=" O   LYS M 121 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 98 through 104
      removed outlier: 3.843A  pdb=" N   ILE O 103 " --> pdb=" O   ILE O  99 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 158 through 164
      removed outlier: 3.622A  pdb=" N   LEU O 162 " --> pdb=" O   THR O 158 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 227 through 238
      removed outlier: 3.504A  pdb=" N   LYS O 232 " --> pdb=" O   LEU O 228 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LYS O 233 " --> pdb=" O   ASP O 229 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR O 235 " --> pdb=" O   GLN O 231 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ASP O 236 " --> pdb=" O   LYS O 232 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS O 237 " --> pdb=" O   LYS O 233 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LEU O 238 " --> pdb=" O   LEU O 234 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.772A  pdb=" N   ALA A 157 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.637A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 11.340A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.772A  pdb=" N   ALA A 157 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.637A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 11.340A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 739 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600
      removed outlier: 7.308A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.658A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680
      removed outlier: 3.718A  pdb=" N   LEU A 866 " --> pdb=" O   ASP A 869 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP A 869 " --> pdb=" O   LEU A 866 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 711 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL A 709 " --> pdb=" O   LEU A 872 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 905 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA9, first strand: chain 'O' and resid 181 through 184
      removed outlier: 7.216A  pdb=" N   LEU O 145 " --> pdb=" O   LEU O 118 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   VAL O 120 " --> pdb=" O   THR O 143 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   THR O 143 " --> pdb=" O   VAL O 120 " (cutoff:3.500A)
      removed outlier: 9.523A  pdb=" N   LEU O 204 " --> pdb=" O   SER O 152 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   ARG O 154 " --> pdb=" O   LEU O 204 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   VAL O 206 " --> pdb=" O   ARG O 154 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU O 156 " --> pdb=" O   VAL O 206 " (cutoff:3.500A)

    456 hydrogen bonds defined for protein.
    1320 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      187 hydrogen bonds
      346 hydrogen bond angles
      0 basepair planarities
      71 basepair parallelities
      125 stacking parallelities
  Total time for adding SS restraints: 4.36

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1941
        1.31 -     1.44: 5740
        1.44 -     1.57: 8071
        1.57 -     1.70: 516
        1.70 -     1.83: 55
  Bond restraints: 16323
  Sorted by residual:
  bond pdb=" C   GLN A 454 "
       pdb=" O   GLN A 454 "
    ideal  model  delta    sigma   weight residual
    1.233  1.185  0.049 1.06e-02 8.90e+03 2.11e+01
  bond pdb=" CG  ARG A 378 "
       pdb=" CD  ARG A 378 "
    ideal  model  delta    sigma   weight residual
    1.520  1.428  0.092 3.00e-02 1.11e+03 9.31e+00
  bond pdb=" CA  PRO A1020 "
       pdb=" CB  PRO A1020 "
    ideal  model  delta    sigma   weight residual
    1.533  1.490  0.043 1.42e-02 4.96e+03 9.20e+00
  bond pdb=" CZ  ARG L  33 "
       pdb=" NH2 ARG L  33 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.98e+00
  bond pdb=" C   VAL A 554 "
       pdb=" O   VAL A 554 "
    ideal  model  delta    sigma   weight residual
    1.237  1.202  0.035 1.19e-02 7.06e+03 8.76e+00
  ... (remaining 16318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 22137
        2.55 -     5.10: 1158
        5.10 -     7.64: 44
        7.64 -    10.19: 4
       10.19 -    12.74: 3
  Bond angle restraints: 23346
  Sorted by residual:
  angle pdb=" O3'   C B 119 "
        pdb=" P     G B 120 "
        pdb=" O5'   G B 120 "
      ideal   model   delta    sigma   weight residual
     104.00   91.26   12.74 1.50e+00 4.44e-01 7.21e+01
  angle pdb=" C   LYS A 338 "
        pdb=" CA  LYS A 338 "
        pdb=" CB  LYS A 338 "
      ideal   model   delta    sigma   weight residual
     109.84  101.84    8.00 1.50e+00 4.44e-01 2.84e+01
  angle pdb=" CA  LYS A 338 "
        pdb=" C   LYS A 338 "
        pdb=" O   LYS A 338 "
      ideal   model   delta    sigma   weight residual
     120.96  116.03    4.93 1.09e+00 8.42e-01 2.05e+01
  angle pdb=" N   PRO A 530 "
        pdb=" CA  PRO A 530 "
        pdb=" C   PRO A 530 "
      ideal   model   delta    sigma   weight residual
     110.40  117.37   -6.97 1.61e+00 3.86e-01 1.88e+01
  angle pdb=" C4'   A B  49 "
        pdb=" C3'   A B  49 "
        pdb=" C2'   A B  49 "
      ideal   model   delta    sigma   weight residual
     102.60   98.40    4.20 1.00e+00 1.00e+00 1.77e+01
  ... (remaining 23341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 9451
       35.74 -    71.49: 702
       71.49 -   107.23: 112
      107.23 -   142.98: 8
      142.98 -   178.72: 11
  Dihedral angle restraints: 10284
    sinusoidal: 6663
      harmonic: 3621
  Sorted by residual:
  dihedral pdb=" C5'   A B 176 "
           pdb=" C4'   A B 176 "
           pdb=" C3'   A B 176 "
           pdb=" O3'   A B 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   74.89   72.11     1      8.00e+00 1.56e-02 1.04e+02
  dihedral pdb=" C4'   G B 300 "
           pdb=" C3'   G B 300 "
           pdb=" C2'   G B 300 "
           pdb=" C1'   G B 300 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.26  -70.26     1      8.00e+00 1.56e-02 9.93e+01
  dihedral pdb=" C4'   U B 307 "
           pdb=" C3'   U B 307 "
           pdb=" C2'   U B 307 "
           pdb=" C1'   U B 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   34.78  -69.78     1      8.00e+00 1.56e-02 9.82e+01
  ... (remaining 10281 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 2439
       0.117 -    0.233: 393
       0.233 -    0.350: 13
       0.350 -    0.466: 2
       0.466 -    0.583: 3
  Chirality restraints: 2850
  Sorted by residual:
  chirality pdb=" P    DG N  24 "
            pdb=" OP1  DG N  24 "
            pdb=" OP2  DG N  24 "
            pdb=" O5'  DG N  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.93   -0.58 2.00e-01 2.50e+01 8.50e+00
  chirality pdb=" P     G B 163 "
            pdb=" OP1   G B 163 "
            pdb=" OP2   G B 163 "
            pdb=" O5'   G B 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 6.95e+00
  chirality pdb=" P     C B 238 "
            pdb=" OP1   C B 238 "
            pdb=" OP2   C B 238 "
            pdb=" O5'   C B 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.93   -0.52 2.00e-01 2.50e+01 6.87e+00
  ... (remaining 2847 not shown)

  Planarity restraints: 2013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 142 "   -0.206 2.00e-02 2.50e+03   1.06e-01 2.52e+02
        pdb=" N1    C B 142 "    0.050 2.00e-02 2.50e+03
        pdb=" C2    C B 142 "    0.056 2.00e-02 2.50e+03
        pdb=" O2    C B 142 "    0.053 2.00e-02 2.50e+03
        pdb=" N3    C B 142 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    C B 142 "    0.057 2.00e-02 2.50e+03
        pdb=" N4    C B 142 "   -0.180 2.00e-02 2.50e+03
        pdb=" C5    C B 142 "    0.070 2.00e-02 2.50e+03
        pdb=" C6    C B 142 "    0.096 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 307 "   -0.089 2.00e-02 2.50e+03   5.23e-02 6.15e+01
        pdb=" N1    U B 307 "    0.086 2.00e-02 2.50e+03
        pdb=" C2    U B 307 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    U B 307 "    0.050 2.00e-02 2.50e+03
        pdb=" N3    U B 307 "   -0.061 2.00e-02 2.50e+03
        pdb=" C4    U B 307 "   -0.015 2.00e-02 2.50e+03
        pdb=" O4    U B 307 "   -0.016 2.00e-02 2.50e+03
        pdb=" C5    U B 307 "    0.049 2.00e-02 2.50e+03
        pdb=" C6    U B 307 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 291 "   -0.035 2.00e-02 2.50e+03   3.65e-02 3.00e+01
        pdb=" N1    U B 291 "    0.019 2.00e-02 2.50e+03
        pdb=" C2    U B 291 "   -0.036 2.00e-02 2.50e+03
        pdb=" O2    U B 291 "    0.066 2.00e-02 2.50e+03
        pdb=" N3    U B 291 "   -0.051 2.00e-02 2.50e+03
        pdb=" C4    U B 291 "    0.010 2.00e-02 2.50e+03
        pdb=" O4    U B 291 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    U B 291 "    0.043 2.00e-02 2.50e+03
        pdb=" C6    U B 291 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2010 not shown)

  Histogram of nonbonded interaction distances:
        1.31 -     2.03: 4
        2.03 -     2.75: 1149
        2.75 -     3.47: 20457
        3.47 -     4.18: 39942
        4.18 -     4.90: 60697
  Nonbonded interactions: 122249
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 510 "
            pdb=" O2'   C B 313 "
     model   vdw
     1.313 3.040
  nonbonded pdb=" OG  SER A  12 "
            pdb=" O2'   A B  61 "
     model   vdw
     1.827 3.040
  nonbonded pdb=" CA  HIS A 752 "
            pdb=" O6    G B  58 "
     model   vdw
     1.869 3.470
  nonbonded pdb=" C   HIS A 752 "
            pdb=" O6    G B  58 "
     model   vdw
     2.026 3.270
  nonbonded pdb=" O   PHE A1021 "
            pdb=" O2'   U B 312 "
     model   vdw
     2.051 3.040
  ... (remaining 122244 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     18.350
  Find NCS groups from input model:        0.050
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
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      :  0.009   0.092  16323  Z= 0.554
  Angle     :  1.229  12.740  23346  Z= 0.785
  Chirality :  0.083   0.583   2850
  Planarity :  0.012   0.149   2013
  Dihedral  : 22.034 178.722   7938
  Min Nonbonded Distance : 1.313

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.28 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.96 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.06 (0.19), residues: 1227
  helix: -1.82 (0.17), residues: 545
  sheet: -1.95 (0.43), residues: 106
  loop : -2.19 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.003   ARG A 470 
 TYR   0.057   0.007   TYR A 576 
 PHE   0.056   0.008   PHE A 708 
 TRP   0.052   0.010   TRP A 547 
 HIS   0.020   0.004   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00883 (16323)
  covalent geometry    : angle       1.22859 (23346)
  hydrogen bonds       : bond        0.27646 (  630)
  hydrogen bonds       : angle       8.37545 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7969 (tp30)
REVERT: A  384 GLN cc_start: 0.7157 (tt0) cc_final: 0.6572 (pm20)
REVERT: A  395 GLU cc_start: 0.9577 (tt0) cc_final: 0.9359 (tm-30)
REVERT: A  399 ASN cc_start: 0.8169 (m-40) cc_final: 0.7852 (m110)
REVERT: A  489 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8818 (mmp80)
REVERT: A  555 GLU cc_start: 0.8815 (tp30) cc_final: 0.8341 (tp30)
REVERT: A  580 VAL cc_start: 0.7367 (p) cc_final: 0.6942 (m)
REVERT: A  775 GLN cc_start: 0.8457 (mt0) cc_final: 0.8218 (mp10)
REVERT: A  900 LEU cc_start: 0.8477 (mp) cc_final: 0.8031 (tt)
REVERT: L   63 ILE cc_start: 0.6042 (tt) cc_final: 0.5609 (pt)
REVERT: L   75 LYS cc_start: 0.6533 (tptt) cc_final: 0.6277 (ttpp)
REVERT: M   50 HIS cc_start: 0.5946 (m-70) cc_final: 0.5599 (m170)
REVERT: M   63 MET cc_start: 0.8680 (mtt) cc_final: 0.7844 (tpt)
REVERT: M   66 PHE cc_start: 0.8166 (m-80) cc_final: 0.7607 (m-80)
REVERT: O   98 TRP cc_start: 0.7390 (p-90) cc_final: 0.6866 (p-90)
REVERT: O  154 ARG cc_start: 0.5176 (ttp80) cc_final: 0.4966 (tmt-80)
REVERT: O  159 ARG cc_start: 0.8252 (ttt180) cc_final: 0.7942 (mmm160)
REVERT: O  169 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7147 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1913
  time to fit residues: 48.8790
Evaluate side-chains
  97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.0570
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0470
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 460 GLN
A 879 HIS
** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 GLN
L  74 ASN
O 116 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.115633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.097477 restraints weight = 78263.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.096921 restraints weight = 55902.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.096687 restraints weight = 52420.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.097094 restraints weight = 44088.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.097090 restraints weight = 37329.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16323  Z= 0.141
  Angle     :  0.697  11.153  23346  Z= 0.349
  Chirality :  0.039   0.257   2850
  Planarity :  0.005   0.067   2013
  Dihedral  : 23.792 176.295   5519
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.18 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  6.42 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.22), residues: 1227
  helix:  0.25 (0.20), residues: 577
  sheet: -1.26 (0.41), residues: 122
  loop : -1.58 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 607 
 TYR   0.013   0.001   TYR A 707 
 PHE   0.011   0.002   PHE A 870 
 TRP   0.039   0.002   TRP O 167 
 HIS   0.005   0.001   HIS A 879 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (16323)
  covalent geometry    : angle       0.69710 (23346)
  hydrogen bonds       : bond        0.05225 (  630)
  hydrogen bonds       : angle       4.35968 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   63 ILE cc_start: 0.6549 (tt) cc_final: 0.6324 (pt)
REVERT: M   69 ASP cc_start: 0.7793 (p0) cc_final: 0.6509 (p0)
REVERT: M   70 ILE cc_start: 0.8585 (mm) cc_final: 0.8118 (mt)
REVERT: O   98 TRP cc_start: 0.6638 (p-90) cc_final: 0.6239 (p-90)
  outliers start: 12
  outliers final: 8
  residues processed: 127
  average time/residue: 0.1772
  time to fit residues: 30.9721
Evaluate side-chains
  80 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  839 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain L residue   69 ASN
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   96 GLN
Chi-restraints excluded: chain O residue  150 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 146 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 148 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 135 optimal weight:    0.0570
   chunk 60 optimal weight:    8.9990
   overall best weight:    2.6106

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

Flipped N/Q/H residues before XYZ refinement:
A 546 HIS
A 876 HIS
A 969 ASN
A 983 HIS
A1018 GLN
** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  25 GLN
** M  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN
** M  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.108473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.087345 restraints weight = 75021.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.087196 restraints weight = 60262.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.087552 restraints weight = 42873.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.088215 restraints weight = 36843.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.088013 restraints weight = 35429.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16323  Z= 0.213
  Angle     :  0.744  11.336  23346  Z= 0.374
  Chirality :  0.041   0.230   2850
  Planarity :  0.006   0.074   2013
  Dihedral  : 23.938 173.334   5519
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  8.19 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.22), residues: 1227
  helix:  0.23 (0.21), residues: 583
  sheet: -0.70 (0.46), residues: 116
  loop : -1.33 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG L  72 
 TYR   0.031   0.002   TYR A 552 
 PHE   0.026   0.003   PHE A 561 
 TRP   0.013   0.002   TRP O  98 
 HIS   0.008   0.002   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (16323)
  covalent geometry    : angle       0.74404 (23346)
  hydrogen bonds       : bond        0.06040 (  630)
  hydrogen bonds       : angle       4.36073 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6546 (p)
REVERT: A  787 ARG cc_start: 0.6959 (mmt-90) cc_final: 0.6482 (mmt180)
  outliers start: 24
  outliers final: 17
  residues processed: 96
  average time/residue: 0.1751
  time to fit residues: 23.6519
Evaluate side-chains
  77 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  700 GLN
Chi-restraints excluded: chain A residue  718 ASP
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  839 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain L residue   69 ASN
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   42 VAL
Chi-restraints excluded: chain M residue   96 GLN
Chi-restraints excluded: chain O residue  150 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 140 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   chunk 90 optimal weight:    0.8980
   chunk 123 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
A 781 GLN
A 816 HIS
** M  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  85 ASN
M  96 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.110722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.090136 restraints weight = 75238.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.090195 restraints weight = 55668.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.090020 restraints weight = 43074.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.090222 restraints weight = 41896.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.090297 restraints weight = 37491.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6575
moved from start:          0.5590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  16323  Z= 0.113
  Angle     :  0.573   9.128  23346  Z= 0.288
  Chirality :  0.035   0.212   2850
  Planarity :  0.004   0.060   2013
  Dihedral  : 23.673 168.537   5519
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.18 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.06 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.23), residues: 1227
  helix:  0.89 (0.21), residues: 580
  sheet: -0.34 (0.47), residues: 117
  loop : -1.00 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG O 208 
 TYR   0.013   0.001   TYR A 707 
 PHE   0.015   0.001   PHE M  66 
 TRP   0.011   0.001   TRP A 547 
 HIS   0.005   0.001   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (16323)
  covalent geometry    : angle       0.57343 (23346)
  hydrogen bonds       : bond        0.04095 (  630)
  hydrogen bonds       : angle       3.81237 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  787 ARG cc_start: 0.6976 (mmt-90) cc_final: 0.6566 (mmt180)
REVERT: L   78 ARG cc_start: 0.7139 (ttt180) cc_final: 0.6788 (tpt-90)
REVERT: O   98 TRP cc_start: 0.6481 (p-90) cc_final: 0.6232 (p-90)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1795
  time to fit residues: 20.3985
Evaluate side-chains
  69 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  718 ASP
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  839 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain O residue  150 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 105 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0010
   chunk 53 optimal weight:    7.9990
   chunk 114 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 134 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   overall best weight:    2.7994

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1022 HIS
O 122 GLN
** O 190 HIS ** 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 = 0.4408 r_free = 0.4408 target = 0.106407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.084962 restraints weight = 74521.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.084956 restraints weight = 56014.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.085175 restraints weight = 43627.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.085158 restraints weight = 39020.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.085234 restraints weight = 36192.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.6641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  16323  Z= 0.214
  Angle     :  0.685   9.665  23346  Z= 0.344
  Chirality :  0.039   0.250   2850
  Planarity :  0.005   0.057   2013
  Dihedral  : 23.950 167.858   5519
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.40 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 10.24 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.23), residues: 1227
  helix:  0.57 (0.21), residues: 585
  sheet: -0.38 (0.47), residues: 118
  loop : -0.94 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A   8 
 TYR   0.023   0.002   TYR A 552 
 PHE   0.020   0.002   PHE M  71 
 TRP   0.012   0.002   TRP A 478 
 HIS   0.007   0.002   HIS A 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (16323)
  covalent geometry    : angle       0.68527 (23346)
  hydrogen bonds       : bond        0.05271 (  630)
  hydrogen bonds       : angle       4.28589 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  384 GLN cc_start: 0.4085 (OUTLIER) cc_final: 0.3794 (pp30)
REVERT: A  872 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.5945 (tp)
REVERT: A  904 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7412 (t)
REVERT: L   78 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7194 (tpt-90)
REVERT: O   98 TRP cc_start: 0.6691 (p-90) cc_final: 0.6346 (p-90)
  outliers start: 26
  outliers final: 14
  residues processed: 92
  average time/residue: 0.1690
  time to fit residues: 21.8393
Evaluate side-chains
  78 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  700 GLN
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  970 MET
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain L residue   69 ASN
Chi-restraints excluded: chain O residue  150 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 124 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 137 optimal weight:   10.0000
   chunk 75 optimal weight:    0.2980
   chunk 104 optimal weight:    7.9990
   chunk 135 optimal weight:   40.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 HIS
** M  50 HIS ** 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 = 0.4434 r_free = 0.4434 target = 0.107762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.086381 restraints weight = 74674.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.086080 restraints weight = 52254.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.086626 restraints weight = 42159.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.086462 restraints weight = 35322.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.086588 restraints weight = 34837.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.6934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16323  Z= 0.136
  Angle     :  0.587   9.150  23346  Z= 0.293
  Chirality :  0.036   0.222   2850
  Planarity :  0.004   0.054   2013
  Dihedral  : 23.820 166.192   5519
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.50 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.10 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.23), residues: 1227
  helix:  0.89 (0.21), residues: 587
  sheet: -0.37 (0.45), residues: 125
  loop : -0.95 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG O 208 
 TYR   0.016   0.001   TYR A 552 
 PHE   0.017   0.001   PHE M  71 
 TRP   0.009   0.001   TRP A 547 
 HIS   0.010   0.001   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (16323)
  covalent geometry    : angle       0.58694 (23346)
  hydrogen bonds       : bond        0.04257 (  630)
  hydrogen bonds       : angle       3.98329 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6599 (tp)
REVERT: A  384 GLN cc_start: 0.3891 (OUTLIER) cc_final: 0.3665 (pp30)
REVERT: A  775 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8172 (mp10)
REVERT: A  872 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6026 (tp)
REVERT: L   78 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7180 (tpt-90)
REVERT: O   98 TRP cc_start: 0.6705 (p-90) cc_final: 0.6292 (p-90)
REVERT: O  229 ASP cc_start: 0.5781 (p0) cc_final: 0.4884 (t0)
  outliers start: 19
  outliers final: 8
  residues processed: 80
  average time/residue: 0.1557
  time to fit residues: 17.9144
Evaluate side-chains
  71 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  775 GLN
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1088 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 105 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 143 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 HIS
** M  50 HIS ** 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 = 0.4382 r_free = 0.4382 target = 0.104577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.083535 restraints weight = 74130.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.083947 restraints weight = 55416.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.084114 restraints weight = 40770.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.084024 restraints weight = 37463.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.084077 restraints weight = 35138.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.7961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  16323  Z= 0.223
  Angle     :  0.703   9.598  23346  Z= 0.352
  Chirality :  0.040   0.258   2850
  Planarity :  0.005   0.056   2013
  Dihedral  : 24.175 173.236   5519
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.97 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.22 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.23), residues: 1227
  helix:  0.30 (0.20), residues: 608
  sheet:  0.10 (0.51), residues: 106
  loop : -1.07 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A   8 
 TYR   0.018   0.002   TYR A 552 
 PHE   0.018   0.002   PHE A 693 
 TRP   0.028   0.002   TRP O 167 
 HIS   0.007   0.002   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (16323)
  covalent geometry    : angle       0.70263 (23346)
  hydrogen bonds       : bond        0.05568 (  630)
  hydrogen bonds       : angle       4.49952 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.2693 (OUTLIER) cc_final: 0.2492 (pp)
REVERT: A  384 GLN cc_start: 0.4310 (OUTLIER) cc_final: 0.4099 (pp30)
REVERT: A  872 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6068 (tp)
REVERT: L   78 ARG cc_start: 0.7632 (ttt180) cc_final: 0.7408 (ttt180)
REVERT: O   98 TRP cc_start: 0.6674 (p-90) cc_final: 0.6190 (p-90)
REVERT: O  229 ASP cc_start: 0.6069 (p0) cc_final: 0.4961 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 85
  average time/residue: 0.1577
  time to fit residues: 19.1438
Evaluate side-chains
  73 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   47 PHE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  922 MET
Chi-restraints excluded: chain A residue 1088 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 106 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0020
   overall best weight:    2.3794

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 GLN
** M  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.105546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.084777 restraints weight = 74234.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.083984 restraints weight = 56902.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.083924 restraints weight = 44684.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.084073 restraints weight = 44808.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.084211 restraints weight = 39072.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.8214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  16323  Z= 0.174
  Angle     :  0.629   9.112  23346  Z= 0.313
  Chirality :  0.037   0.237   2850
  Planarity :  0.004   0.056   2013
  Dihedral  : 24.042 172.131   5519
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.24 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.41 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.23), residues: 1227
  helix:  0.56 (0.21), residues: 598
  sheet:  0.29 (0.53), residues: 106
  loop : -1.06 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG O 208 
 TYR   0.017   0.001   TYR A 552 
 PHE   0.014   0.002   PHE M  66 
 TRP   0.030   0.002   TRP O 167 
 HIS   0.008   0.002   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (16323)
  covalent geometry    : angle       0.62926 (23346)
  hydrogen bonds       : bond        0.04798 (  630)
  hydrogen bonds       : angle       4.28259 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.2570 (OUTLIER) cc_final: 0.2364 (pp)
REVERT: A  593 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6605 (tt)
REVERT: A  872 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6026 (tp)
REVERT: L   78 ARG cc_start: 0.7517 (ttt180) cc_final: 0.6978 (tpt-90)
REVERT: O   98 TRP cc_start: 0.6904 (p-90) cc_final: 0.6540 (p-90)
REVERT: O  229 ASP cc_start: 0.6352 (p0) cc_final: 0.5278 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1448
  time to fit residues: 17.7801
Evaluate side-chains
  76 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   47 PHE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  922 MET
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain L residue   69 ASN
Chi-restraints excluded: chain M residue   96 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 129 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    0.2980
   chunk 111 optimal weight:    9.9990
   chunk 90 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
** M  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 190 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.104499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.083538 restraints weight = 73458.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.083052 restraints weight = 52566.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.083076 restraints weight = 40877.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.083270 restraints weight = 40893.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.083377 restraints weight = 35243.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.8761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16323  Z= 0.199
  Angle     :  0.669  10.257  23346  Z= 0.334
  Chirality :  0.039   0.325   2850
  Planarity :  0.005   0.055   2013
  Dihedral  : 24.109 176.144   5519
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.65 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.43 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.23), residues: 1227
  helix:  0.51 (0.21), residues: 596
  sheet:  0.31 (0.53), residues: 106
  loop : -1.06 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O 208 
 TYR   0.017   0.002   TYR A 552 
 PHE   0.042   0.002   PHE M  71 
 TRP   0.014   0.002   TRP O 167 
 HIS   0.007   0.002   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (16323)
  covalent geometry    : angle       0.66880 (23346)
  hydrogen bonds       : bond        0.05082 (  630)
  hydrogen bonds       : angle       4.34764 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.2678 (OUTLIER) cc_final: 0.2407 (pp)
REVERT: A  148 VAL cc_start: 0.5452 (t) cc_final: 0.5124 (p)
REVERT: A  787 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7252 (mmt-90)
REVERT: A  872 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6066 (tp)
REVERT: M   58 LYS cc_start: 0.6951 (mmmt) cc_final: 0.6481 (mtpt)
REVERT: O   98 TRP cc_start: 0.7147 (p-90) cc_final: 0.6538 (p-90)
  outliers start: 16
  outliers final: 12
  residues processed: 82
  average time/residue: 0.1316
  time to fit residues: 16.0755
Evaluate side-chains
  77 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   47 PHE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  495 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  922 MET
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain M residue   96 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 126 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 78 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 136 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 134 optimal weight:    9.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 748 GLN
** M  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.107344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.086992 restraints weight = 74601.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.086509 restraints weight = 51800.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.086656 restraints weight = 41762.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.086829 restraints weight = 38816.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.086905 restraints weight = 34131.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.8782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  16323  Z= 0.111
  Angle     :  0.579   8.546  23346  Z= 0.287
  Chirality :  0.035   0.207   2850
  Planarity :  0.005   0.085   2013
  Dihedral  : 23.900 172.030   5519
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.42 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.80 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.24), residues: 1227
  helix:  0.92 (0.21), residues: 592
  sheet:  0.41 (0.53), residues: 104
  loop : -0.87 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 522 
 TYR   0.016   0.001   TYR A 552 
 PHE   0.020   0.001   PHE M  66 
 TRP   0.021   0.001   TRP O 167 
 HIS   0.004   0.001   HIS O 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (16323)
  covalent geometry    : angle       0.57948 (23346)
  hydrogen bonds       : bond        0.04136 (  630)
  hydrogen bonds       : angle       3.97323 ( 1666)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A  872 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5913 (tp)
REVERT: O   98 TRP cc_start: 0.6975 (p-90) cc_final: 0.6755 (p-90)
REVERT: O  229 ASP cc_start: 0.6143 (p0) cc_final: 0.5160 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 80
  average time/residue: 0.1317
  time to fit residues: 15.7957
Evaluate side-chains
  72 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain M residue   96 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 144 optimal weight:   30.0000
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 3 optimal weight:    0.4980
   chunk 116 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 114 optimal weight:   10.0000
   chunk 132 optimal weight:    9.9990
   chunk 72 optimal weight:    0.2980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** M  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  96 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 = 0.4450 r_free = 0.4450 target = 0.107864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.087174 restraints weight = 74595.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.086931 restraints weight = 49967.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.087504 restraints weight = 38438.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.087340 restraints weight = 33723.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.087454 restraints weight = 32599.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
moved from start:          0.8876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  16323  Z= 0.105
  Angle     :  0.562   8.944  23346  Z= 0.278
  Chirality :  0.034   0.199   2850
  Planarity :  0.004   0.057   2013
  Dihedral  : 23.802 171.352   5519
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.91 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.08 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.24), residues: 1227
  helix:  1.10 (0.21), residues: 595
  sheet:  0.43 (0.55), residues: 91
  loop : -0.73 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 865 
 TYR   0.015   0.001   TYR M  38 
 PHE   0.018   0.001   PHE M  66 
 TRP   0.017   0.001   TRP O 167 
 HIS   0.012   0.001   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (16323)
  covalent geometry    : angle       0.56182 (23346)
  hydrogen bonds       : bond        0.04002 (  630)
  hydrogen bonds       : angle       3.83501 ( 1666)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2643.64 seconds
wall clock time: 46 minutes 31.66 seconds (2791.66 seconds total)