Starting phenix.real_space_refine (version: dev)
on Tue Feb 21 07:11:47 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2023/7bg9_12174_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2023/7bg9_12174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2023/7bg9_12174.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2023/7bg9_12174.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2023/7bg9_12174_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2023/7bg9_12174_neut.pdb"
  }
  resolution = 3.8
  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
-------------------------------------------------------------------------------
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=   0.003
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
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   20": "OE1" <-> "OE2"
    Residue "A ARG   29": "NH1" <-> "NH2"
    Residue "A GLU  362": "OE1" <-> "OE2"
    Residue "A PHE  494": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  538": "OE1" <-> "OE2"
    Residue "A GLU  539": "OE1" <-> "OE2"
    Residue "A TYR  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  568": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  576": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  724": "NH1" <-> "NH2"
    Residue "A PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  812": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  894": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  910": "OE1" <-> "OE2"
    Residue "A PHE  928": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  960": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  964": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU   36": "OE1" <-> "OE2"
    Residue "M TYR   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU   77": "OE1" <-> "OE2"
    Residue "L PHE   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU   42": "OE1" <-> "OE2"
    Residue "L GLU   65": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 14233
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 913, 7333
          Classifications: {'peptide': 913}
          Link IDs: {'PTRANS': 51, 'TRANS': 861}
          Chain breaks: 4
    Chain: "N"
      Number of atoms: 127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 127
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    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: "L"
      Number of atoms: 643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 643
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "B"
      Number of atoms: 5431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 5431
          Classifications: {'RNA': 256}
          Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 10, 'rna3p_pur': 103, 'rna3p_pyr': 130}
          Link IDs: {'rna2p': 23, 'rna3p': 232}
          Chain breaks: 3
  Time building chain proxies: 8.20, per 1000 atoms: 0.58
  Number of scatterers: 14233
  At special positions: 0
  Unit cell: (134.31, 139.86, 135.42, 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      37     16.00
     P     262     15.00
     O    3320      8.00
     N    2586      7.00
     C    8028      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  - 3.50
        Amino acid           : False - 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: 6.59
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      54.7% alpha, 6.5% beta
      70 base pairs and 128 stacking pairs defined.
    Time for finding SS restraints: 4.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 22
      removed outlier: 3.727A  pdb=" N   ARG A  15 " --> pdb=" O   ARG A  11 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   SER A  16 " --> pdb=" O   SER A  12 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A  19 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A  21 " --> pdb=" O   HIS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 78 through 88
      removed outlier: 4.297A  pdb=" N   VAL A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ARG A  87 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 100
      removed outlier: 4.322A  pdb=" N   PHE A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 95 through 100'
    Processing helix  chain 'A' and resid 133 through 145
      removed outlier: 3.543A  pdb=" N   LEU A 141 " --> pdb=" O   TRP A 137 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ARG A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 4.113A  pdb=" N   ALA A 154 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 179
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 3.630A  pdb=" N   LYS A 329 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
      removed outlier: 3.523A  pdb=" N   LEU A 347 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 366
      removed outlier: 4.184A  pdb=" N   ARG A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 4.044A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 3.593A  pdb=" N   VAL A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 470
      removed outlier: 4.117A  pdb=" N   GLY A 463 " --> pdb=" O   TRP A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 4.012A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLY A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 474 through 479'
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 4.259A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 558
      removed outlier: 3.599A  pdb=" N   ILE A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 542 " --> pdb=" O   GLU A 538 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TRP A 547 " --> pdb=" O   LYS A 543 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A 556 " --> pdb=" O   TYR A 552 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 557 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 595
      removed outlier: 3.574A  pdb=" N   LYS A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LYS A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 595 " --> pdb=" O   GLN A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 610
      removed outlier: 3.839A  pdb=" N   GLN A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 3.509A  pdb=" N   VAL A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ARG A 669 " --> pdb=" O   LEU A 665 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA A 670 " --> pdb=" O   ASN A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 683 through 697
      removed outlier: 3.587A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
      removed outlier: 4.204A  pdb=" N   LEU A 725 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 731 " --> pdb=" O   GLU A 727 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE A 732 " --> pdb=" O   VAL A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 781
    Processing helix  chain 'A' and resid 782 through 784
      No H-bonds generated for 'chain 'A' and resid 782 through 784'
    Processing helix  chain 'A' and resid 801 through 815
      removed outlier: 3.706A  pdb=" N   PHE A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 854
      removed outlier: 3.541A  pdb=" N   CYS A 842 " --> pdb=" O   SER A 838 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR A 846 " --> pdb=" O   CYS A 842 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN A 851 " --> pdb=" O   GLY A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 889
      removed outlier: 3.843A  pdb=" N   ALA A 880 " --> pdb=" O   HIS A 876 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS A 881 " --> pdb=" O   LEU A 877 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 882 " --> pdb=" O   THR A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 958
      removed outlier: 3.854A  pdb=" N   SER A 957 " --> pdb=" O   SER A 953 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 958 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 953 through 958'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.810A  pdb=" N   ARG A 972 " --> pdb=" O   ARG A 968 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LEU A 980 " --> pdb=" O   GLY A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 3.725A  pdb=" N   LEU A 987 " --> pdb=" O   HIS A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1017
      removed outlier: 4.017A  pdb=" N   THR A 999 " --> pdb=" O   GLN A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1027
      removed outlier: 3.531A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1024 through 1027'
    Processing helix  chain 'A' and resid 1028 through 1052
      removed outlier: 4.230A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A1033 " --> pdb=" O   PRO A1029 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASP A1038 " --> pdb=" O   ARG A1034 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A1042 " --> pdb=" O   ASP A1038 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A1049 " --> pdb=" O   SER A1045 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1083
      removed outlier: 4.412A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   HIS A1075 " --> pdb=" O   GLN A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1090
      removed outlier: 3.903A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1106
      removed outlier: 3.901A  pdb=" N   ALA A1099 " --> pdb=" O   SER A1095 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.510A  pdb=" N   THR A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA A1114 " --> pdb=" O   THR A1110 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A1118 " --> pdb=" O   ALA A1114 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 38 through 50
      removed outlier: 3.801A  pdb=" N   TYR M  43 " --> pdb=" O   SER M  39 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 4.108A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL M  67 " --> pdb=" O   MET M  63 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ASN M  68 " --> pdb=" O   ASN M  64 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE M  74 " --> pdb=" O   ILE M  70 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 4.193A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL M  99 " --> pdb=" O   ILE M  95 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU M 101 " --> pdb=" O   THR M  97 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 105 through 124
      removed outlier: 3.550A  pdb=" N   LYS M 109 " --> pdb=" O   GLY M 105 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS M 121 " --> pdb=" O   LYS M 117 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 23
    Processing helix  chain 'L' and resid 27 through 35
      removed outlier: 3.517A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 74
      removed outlier: 4.561A  pdb=" N   VAL L  50 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR L  51 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL L  55 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU L  56 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR L  58 " --> pdb=" O   ALA L  54 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU L  64 " --> pdb=" O   THR L  60 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA L  67 " --> pdb=" O   ILE L  63 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASP L  73 " --> pdb=" O   ASN L  69 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ASN L  74 " --> pdb=" O   ALA L  70 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 91
      removed outlier: 3.810A  pdb=" N   ALA L  87 " --> pdb=" O   HIS L  83 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG L  89 " --> pdb=" O   GLN L  85 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 92 through 98
      removed outlier: 3.596A  pdb=" N   LEU L  97 " --> pdb=" O   GLU L  93 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 4.151A  pdb=" N   LEU A  24 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 600
    Processing sheet with id=AA4, first strand: chain 'A' and resid 619 through 625
    Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 866
      removed outlier: 3.722A  pdb=" N   LEU A 866 " --> pdb=" O   ASP A 869 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 711 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 905 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 755 through 761
      removed outlier: 3.598A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 928 through 930
    Processing sheet with id=AA8, first strand: chain 'M' and resid 89 through 90
      removed outlier: 3.757A  pdb=" N   ILE M  90 " --> pdb=" O   ARG L  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    339 hydrogen bonds defined for protein.
    972 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      182 hydrogen bonds
      350 hydrogen bond angles
      0 basepair planarities
      70 basepair parallelities
      128 stacking parallelities
  Total time for adding SS restraints: 7.61

  Time building geometry restraints manager: 7.05 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1592
        1.29 -     1.43: 5038
        1.43 -     1.56: 7769
        1.56 -     1.70: 613
        1.70 -     1.84: 51
  Bond restraints: 15063
  Sorted by residual:
  bond pdb=" CA  VAL A 529 "
       pdb=" C   VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.524  1.622 -0.097 1.05e-02 9.07e+03 8.57e+01
  bond pdb=" C   VAL A 529 "
       pdb=" N   PRO A 530 "
    ideal  model  delta    sigma   weight residual
    1.328  1.441 -0.113 1.25e-02 6.40e+03 8.22e+01
  bond pdb=" C   PHE A 560 "
       pdb=" O   PHE A 560 "
    ideal  model  delta    sigma   weight residual
    1.235  1.148  0.088 1.02e-02 9.61e+03 7.37e+01
  bond pdb=" C   GLN A1023 "
       pdb=" O   GLN A1023 "
    ideal  model  delta    sigma   weight residual
    1.235  1.327 -0.092 1.14e-02 7.69e+03 6.49e+01
  bond pdb=" CA  ILE A1004 "
       pdb=" C   ILE A1004 "
    ideal  model  delta    sigma   weight residual
    1.524  1.439  0.085 1.22e-02 6.72e+03 4.84e+01
  ... (remaining 15058 not shown)

  Histogram of bond angle deviations from ideal:
       97.72 -   106.00: 1668
      106.00 -   114.29: 8480
      114.29 -   122.57: 8542
      122.57 -   130.86: 2867
      130.86 -   139.14: 85
  Bond angle restraints: 21642
  Sorted by residual:
  angle pdb=" N   LYS A 410 "
        pdb=" CA  LYS A 410 "
        pdb=" C   LYS A 410 "
      ideal   model   delta    sigma   weight residual
     112.68   99.30   13.38 1.33e+00 5.65e-01 1.01e+02
  angle pdb=" N   ASP A 337 "
        pdb=" CA  ASP A 337 "
        pdb=" C   ASP A 337 "
      ideal   model   delta    sigma   weight residual
     111.02  123.23  -12.21 1.22e+00 6.72e-01 1.00e+02
  angle pdb=" N   PHE A 561 "
        pdb=" CA  PHE A 561 "
        pdb=" C   PHE A 561 "
      ideal   model   delta    sigma   weight residual
     108.76  125.23  -16.47 1.69e+00 3.50e-01 9.50e+01
  angle pdb=" C   VAL A 529 "
        pdb=" N   PRO A 530 "
        pdb=" CA  PRO A 530 "
      ideal   model   delta    sigma   weight residual
     120.85  110.36   10.49 1.08e+00 8.57e-01 9.44e+01
  angle pdb=" N   LYS A 338 "
        pdb=" CA  LYS A 338 "
        pdb=" C   LYS A 338 "
      ideal   model   delta    sigma   weight residual
     111.71  122.61  -10.90 1.15e+00 7.56e-01 8.99e+01
  ... (remaining 21637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.65: 8140
       35.65 -    71.29: 307
       71.29 -   106.94: 28
      106.94 -   142.59: 6
      142.59 -   178.24: 7
  Dihedral angle restraints: 8488
    sinusoidal: 5335
      harmonic: 3153
  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   73.18   73.82     1      8.00e+00 1.56e-02 1.08e+02
  dihedral pdb=" O4'   U B 316 "
           pdb=" C1'   U B 316 "
           pdb=" N1    U B 316 "
           pdb=" C2    U B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.07 -176.07     1      1.50e+01 4.44e-03 8.52e+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   23.52  -58.52     1      8.00e+00 1.56e-02 7.17e+01
  ... (remaining 8485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.156: 2269
       0.156 -    0.313: 356
       0.313 -    0.469: 28
       0.469 -    0.625: 2
       0.625 -    0.782: 3
  Chirality restraints: 2658
  Sorted by residual:
  chirality pdb=" C3'   U B 312 "
            pdb=" C4'   U B 312 "
            pdb=" O3'   U B 312 "
            pdb=" C2'   U B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.70   -0.78 2.00e-01 2.50e+01 1.53e+01
  chirality pdb=" C3'   G B 300 "
            pdb=" C4'   G B 300 "
            pdb=" O3'   G B 300 "
            pdb=" C2'   G B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.07   -0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" C3'   A B 176 "
            pdb=" C4'   A B 176 "
            pdb=" O3'   A B 176 "
            pdb=" C2'   A B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.11   -0.63 2.00e-01 2.50e+01 9.94e+00
  ... (remaining 2655 not shown)

  Planarity restraints: 1784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA N  15 "    0.077 2.00e-02 2.50e+03   3.25e-02 2.90e+01
        pdb=" N9   DA N  15 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8   DA N  15 "   -0.015 2.00e-02 2.50e+03
        pdb=" N7   DA N  15 "   -0.018 2.00e-02 2.50e+03
        pdb=" C5   DA N  15 "   -0.018 2.00e-02 2.50e+03
        pdb=" C6   DA N  15 "    0.028 2.00e-02 2.50e+03
        pdb=" N6   DA N  15 "    0.039 2.00e-02 2.50e+03
        pdb=" N1   DA N  15 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2   DA N  15 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DA N  15 "   -0.017 2.00e-02 2.50e+03
        pdb=" C4   DA N  15 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 177 "   -0.073 2.00e-02 2.50e+03   3.57e-02 2.86e+01
        pdb=" N1    U B 177 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    U B 177 "    0.023 2.00e-02 2.50e+03
        pdb=" O2    U B 177 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    U B 177 "    0.021 2.00e-02 2.50e+03
        pdb=" C4    U B 177 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U B 177 "   -0.051 2.00e-02 2.50e+03
        pdb=" C5    U B 177 "    0.018 2.00e-02 2.50e+03
        pdb=" C6    U B 177 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 547 "    0.043 2.00e-02 2.50e+03   3.25e-02 2.64e+01
        pdb=" CG  TRP A 547 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 547 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 547 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 547 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 547 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 547 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 547 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 547 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 547 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1781 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.19: 6
        2.19 -     2.87: 4325
        2.87 -     3.55: 19210
        3.55 -     4.22: 34638
        4.22 -     4.90: 50134
  Nonbonded interactions: 108313
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP A 510 "
            pdb=" CE1 HIS A1022 "
     model   vdw
     1.518 3.340
  nonbonded pdb=" CB  PRO A  23 "
            pdb=" CZ3 TRP A  60 "
     model   vdw
     1.745 3.740
  nonbonded pdb=" CE2 TRP A 510 "
            pdb=" CE1 HIS A1022 "
     model   vdw
     1.921 3.480
  nonbonded pdb=" ND1 HIS A1022 "
            pdb=" O2'   U B 312 "
     model   vdw
     1.946 2.520
  nonbonded pdb=" NE1 TRP A 510 "
            pdb=" NE2 HIS A1022 "
     model   vdw
     2.130 3.200
  ... (remaining 108308 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     262      5.49       5
     S      37      5.16       5
     C    8028      2.51       5
     N    2586      2.21       5
     O    3320      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.240
  Check model and map are aligned:         0.220
  Process input model:                     44.900
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.140
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
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      :  0.013   0.143  15063  Z= 0.854
  Angle     :  1.642  16.474  21642  Z= 1.041
  Chirality :  0.110   0.782   2658
  Planarity :  0.009   0.101   1784
  Dihedral  : 17.679 178.236   6448
  Min Nonbonded Distance : 1.518

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  1.59 %
    Allowed  : 11.95 %
    Favored  : 86.46 %
  Rotamer Outliers :  0.75 %
  Cbeta Deviations :  0.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.05 (0.20), residues: 1071
  helix: -3.42 (0.15), residues: 461
  sheet: -3.45 (0.47), residues: 66
  loop : -3.29 (0.24), residues: 544

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 184
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 190
  average time/residue: 0.3792
  time to fit residues: 95.0133
Evaluate side-chains
  111 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 1.341 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1236
  time to fit residues: 1.8026
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:   20.0000
   chunk 100 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    0.3980
   chunk 53 optimal weight:   10.0000
   chunk 104 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 120 optimal weight:   30.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A  40 GLN
A 412 HIS
A 454 GLN
A 546 HIS
** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 748 GLN
A 990 GLN
A 995 GLN
A1024 GLN
A1100 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15063  Z= 0.201
  Angle     :  0.733   9.453  21642  Z= 0.373
  Chirality :  0.039   0.284   2658
  Planarity :  0.006   0.072   1784
  Dihedral  : 16.707 179.405   4340
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer Outliers :  3.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.23), residues: 1071
  helix: -1.35 (0.20), residues: 519
  sheet: -2.73 (0.48), residues: 80
  loop : -2.78 (0.27), residues: 472

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 32
  outliers final: 9
  residues processed: 140
  average time/residue: 0.3099
  time to fit residues: 61.2720
Evaluate side-chains
  101 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 1.031 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1186
  time to fit residues: 3.2032
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 120 optimal weight:   30.0000
   chunk 130 optimal weight:    8.9990
   chunk 107 optimal weight:    9.9990
   chunk 119 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 97 optimal weight:   20.0000
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A 762 HIS
A 799 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15063  Z= 0.283
  Angle     :  0.731   8.585  21642  Z= 0.373
  Chirality :  0.039   0.288   2658
  Planarity :  0.006   0.059   1784
  Dihedral  : 16.631 177.629   4340
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer Outliers :  3.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.25), residues: 1071
  helix: -0.38 (0.22), residues: 514
  sheet: -2.17 (0.54), residues: 76
  loop : -2.66 (0.27), residues: 481

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 31
  outliers final: 18
  residues processed: 114
  average time/residue: 0.2788
  time to fit residues: 47.1027
Evaluate side-chains
  108 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.313 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 0
  residues processed: 18
  average time/residue: 0.1688
  time to fit residues: 6.8080
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 119 optimal weight:   20.0000
   chunk 90 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 57 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 121 optimal weight:    9.9990
   chunk 128 optimal weight:   20.0000
   chunk 63 optimal weight:    0.0000
   chunk 115 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A 736 GLN
A 925 HIS
M  50 HIS
M  96 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039  15063  Z= 0.151
  Angle     :  0.607   8.770  21642  Z= 0.309
  Chirality :  0.035   0.247   2658
  Planarity :  0.005   0.057   1784
  Dihedral  : 16.371 177.855   4340
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer Outliers :  2.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.26), residues: 1071
  helix:  0.31 (0.23), residues: 518
  sheet: -1.89 (0.55), residues: 81
  loop : -2.39 (0.27), residues: 472

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 8
  residues processed: 112
  average time/residue: 0.2593
  time to fit residues: 43.9568
Evaluate side-chains
  96 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 1.312 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1536
  time to fit residues: 3.7966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 95 optimal weight:    0.0870
   chunk 53 optimal weight:    0.0570
   chunk 109 optimal weight:   20.0000
   chunk 88 optimal weight:    0.0470
   chunk 0 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.4376

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A 534 HIS
A 925 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15063  Z= 0.167
  Angle     :  0.602  10.113  21642  Z= 0.303
  Chirality :  0.035   0.239   2658
  Planarity :  0.005   0.052   1784
  Dihedral  : 16.307 178.942   4340
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer Outliers :  1.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.26), residues: 1071
  helix:  0.63 (0.24), residues: 519
  sheet: -1.83 (0.54), residues: 81
  loop : -2.28 (0.27), residues: 471

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 5
  residues processed: 107
  average time/residue: 0.2910
  time to fit residues: 45.3171
Evaluate side-chains
  92 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 1.304 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1255
  time to fit residues: 2.7611
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 115 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 128 optimal weight:   20.0000
   chunk 106 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   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  17 HIS
A 925 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.036  15063  Z= 0.142
  Angle     :  0.582   8.603  21642  Z= 0.293
  Chirality :  0.034   0.186   2658
  Planarity :  0.004   0.054   1784
  Dihedral  : 16.175 178.836   4340
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer Outliers :  0.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.26), residues: 1071
  helix:  0.87 (0.24), residues: 526
  sheet: -1.46 (0.58), residues: 79
  loop : -2.24 (0.28), residues: 466

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 104
  average time/residue: 0.2919
  time to fit residues: 44.5237
Evaluate side-chains
  96 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 1.187 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1449
  time to fit residues: 2.7456
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 124 optimal weight:   50.0000
   chunk 14 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 93 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 108 optimal weight:   30.0000
   chunk 71 optimal weight:    3.9990
   chunk 128 optimal weight:   20.0000
   chunk 80 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A 925 HIS
M  96 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15063  Z= 0.185
  Angle     :  0.608   8.735  21642  Z= 0.305
  Chirality :  0.035   0.208   2658
  Planarity :  0.005   0.049   1784
  Dihedral  : 16.147 179.054   4340
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer Outliers :  1.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.26), residues: 1071
  helix:  0.89 (0.24), residues: 530
  sheet: -1.34 (0.58), residues: 81
  loop : -2.30 (0.27), residues: 460

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 10
  residues processed: 99
  average time/residue: 0.3009
  time to fit residues: 43.5177
Evaluate side-chains
  95 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 1.249 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1899
  time to fit residues: 4.5245
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0170
   chunk 24 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0980
   chunk 11 optimal weight:    0.3980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
M  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.040  15063  Z= 0.135
  Angle     :  0.575   8.922  21642  Z= 0.286
  Chirality :  0.033   0.257   2658
  Planarity :  0.004   0.055   1784
  Dihedral  : 15.995 172.605   4340
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer Outliers :  0.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.26), residues: 1071
  helix:  1.11 (0.24), residues: 526
  sheet: -1.08 (0.60), residues: 79
  loop : -2.17 (0.27), residues: 466

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 99
  average time/residue: 0.3349
  time to fit residues: 47.9767
Evaluate side-chains
  89 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 1.258 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1313
  time to fit residues: 1.9681
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 122 optimal weight:   10.0000
   chunk 112 optimal weight:   20.0000
   chunk 119 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 126 optimal weight:   10.0000
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.5651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.046  15063  Z= 0.322
  Angle     :  0.718   8.912  21642  Z= 0.360
  Chirality :  0.040   0.323   2658
  Planarity :  0.005   0.046   1784
  Dihedral  : 16.531 174.629   4340
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer Outliers :  1.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.25), residues: 1071
  helix:  0.66 (0.23), residues: 518
  sheet: -1.25 (0.58), residues: 81
  loop : -2.31 (0.26), residues: 472

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 7
  residues processed: 90
  average time/residue: 0.3125
  time to fit residues: 40.6361
Evaluate side-chains
  90 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 1.263 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1590
  time to fit residues: 3.4972
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 77 optimal weight:    0.0470
   chunk 59 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 132 optimal weight:   20.0000
   chunk 121 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0980
   chunk 64 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0370
   chunk 112 optimal weight:   20.0000
   overall best weight:    1.0360

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.5915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.050  15063  Z= 0.158
  Angle     :  0.612  10.124  21642  Z= 0.305
  Chirality :  0.035   0.240   2658
  Planarity :  0.004   0.055   1784
  Dihedral  : 16.326 173.966   4340
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer Outliers :  0.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.26), residues: 1071
  helix:  0.96 (0.23), residues: 520
  sheet: -1.23 (0.58), residues: 81
  loop : -2.22 (0.27), residues: 470

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 89
  average time/residue: 0.3351
  time to fit residues: 42.2659
Evaluate side-chains
  81 residues out of total 934 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 1.323 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1292
  time to fit residues: 1.8027
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 105 optimal weight:   10.0000
   chunk 44 optimal weight:    0.5980
   chunk 108 optimal weight:   40.0000
   chunk 13 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
** A1022 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 = 0.4101 r_free = 0.4101 target = 0.115474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.081897 restraints weight = 49520.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.082715 restraints weight = 29325.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.082846 restraints weight = 20889.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.6238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.038  15063  Z= 0.145
  Angle     :  0.598   9.787  21642  Z= 0.295
  Chirality :  0.034   0.224   2658
  Planarity :  0.005   0.119   1784
  Dihedral  : 16.212 174.250   4340
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer Outliers :  0.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.26), residues: 1071
  helix:  1.22 (0.24), residues: 520
  sheet: -1.24 (0.59), residues: 81
  loop : -2.12 (0.27), residues: 470

===============================================================================
Job complete
usr+sys time: 2180.31 seconds
wall clock time: 40 minutes 50.49 seconds (2450.49 seconds total)