Starting phenix.real_space_refine (version: dev)
on Tue Apr  5 23:29:18 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/04_2022/7crw_30458.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/04_2022/7crw_30458.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/04_2022/7crw_30458.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/04_2022/7crw_30458.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/04_2022/7crw_30458.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/04_2022/7crw_30458.pdb"
  }
  resolution = 3.18
  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=   0.002
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "D TYR   87": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  671": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 16613
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 6765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 837, 6765
          Classifications: {'peptide': 837}
          Link IDs: {'PTRANS': 53, 'TRANS': 783}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2225
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 258}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1096
          Classifications: {'peptide': 134}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
    Chain: "C"
      Number of atoms: 6527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 807, 6527
          Classifications: {'peptide': 807}
          Link IDs: {'PTRANS': 53, 'TRANS': 753}
          Chain breaks: 5
  Time building chain proxies: 9.55, per 1000 atoms: 0.57
  Number of scatterers: 16613
  At special positions: 0
  Unit cell: (103.978, 149.601, 113.527, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      79     16.00
     O    3015      8.00
     N    2832      7.00
     C   10687      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: 6.28
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3860

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 35 sheets defined
      18.6% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'D' and resid 29 through 43
    Processing helix  chain 'D' and resid 61 through 65
      removed outlier: 3.500A  pdb=" N   GLY D  65 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 119
    Processing helix  chain 'D' and resid 121 through 132
    Processing helix  chain 'D' and resid 242 through 249
    Processing helix  chain 'D' and resid 340 through 345
    Processing helix  chain 'D' and resid 381 through 383
      No H-bonds generated for 'chain 'D' and resid 381 through 383'
    Processing helix  chain 'D' and resid 391 through 402
      removed outlier: 3.548A  pdb=" N   GLU D 397 " --> pdb=" O   ALA D 393 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG D 400 " --> pdb=" O   GLN D 396 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE D 402 " --> pdb=" O   ALA D 398 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 661 through 670
    Processing helix  chain 'D' and resid 685 through 690
      removed outlier: 3.765A  pdb=" N   GLU D 689 " --> pdb=" O   GLY D 685 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 699 through 715
      removed outlier: 3.785A  pdb=" N   ASP D 703 " --> pdb=" O   VAL D 699 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL D 711 " --> pdb=" O   GLY D 707 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA D 712 " --> pdb=" O   LEU D 708 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLU D 713 " --> pdb=" O   GLN D 709 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 730 through 742
    Processing helix  chain 'D' and resid 757 through 761
      removed outlier: 3.818A  pdb=" N   ALA D 760 " --> pdb=" O   VAL D 757 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR D 761 " --> pdb=" O   TRP D 758 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 757 through 761'
    Processing helix  chain 'D' and resid 762 through 771
      removed outlier: 4.623A  pdb=" N   ARG D 768 " --> pdb=" O   GLY D 764 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 772 through 784
      removed outlier: 3.557A  pdb=" N   ASN D 776 " --> pdb=" O   VAL D 772 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   GLN D 778 " --> pdb=" O   GLU D 774 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLY D 779 " --> pdb=" O   ASN D 775 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 785 through 792
      removed outlier: 4.098A  pdb=" N   VAL D 789 " --> pdb=" O   ALA D 786 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   GLU D 790 " --> pdb=" O   LEU D 787 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 812 through 824
    Processing helix  chain 'D' and resid 843 through 862
    Processing helix  chain 'A' and resid 887 through 893
      removed outlier: 4.166A  pdb=" N   PHE A 891 " --> pdb=" O   ALA A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 900
      removed outlier: 3.655A  pdb=" N   HIS A 899 " --> pdb=" O   PRO A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 915
      No H-bonds generated for 'chain 'A' and resid 913 through 915'
    Processing helix  chain 'A' and resid 1012 through 1025
    Processing helix  chain 'B' and resid 1013 through 1025
      removed outlier: 3.609A  pdb=" N   LYS B1017 " --> pdb=" O   CYS B1013 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU B1021 " --> pdb=" O   LYS B1017 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 43
    Processing helix  chain 'C' and resid 242 through 249
    Processing helix  chain 'C' and resid 293 through 297
    Processing helix  chain 'C' and resid 340 through 345
    Processing helix  chain 'C' and resid 381 through 383
      No H-bonds generated for 'chain 'C' and resid 381 through 383'
    Processing helix  chain 'C' and resid 391 through 399
      removed outlier: 3.573A  pdb=" N   GLN C 396 " --> pdb=" O   GLU C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 661 through 670
      removed outlier: 3.747A  pdb=" N   GLY C 670 " --> pdb=" O   LEU C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 688 through 692
      removed outlier: 3.684A  pdb=" N   LEU C 692 " --> pdb=" O   GLU C 689 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 699 through 715
      removed outlier: 3.601A  pdb=" N   ASP C 703 " --> pdb=" O   VAL C 699 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR C 710 " --> pdb=" O   GLU C 706 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 730 through 742
    Processing helix  chain 'C' and resid 757 through 761
      removed outlier: 3.802A  pdb=" N   ALA C 760 " --> pdb=" O   VAL C 757 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 762 through 771
      removed outlier: 4.218A  pdb=" N   ARG C 768 " --> pdb=" O   GLY C 764 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR C 769 " --> pdb=" O   TYR C 765 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 772 through 775
    Processing helix  chain 'C' and resid 776 through 782
      removed outlier: 4.131A  pdb=" N   GLU C 781 " --> pdb=" O   GLN C 777 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 784 through 792
      removed outlier: 4.540A  pdb=" N   VAL C 789 " --> pdb=" O   ALA C 786 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   GLU C 790 " --> pdb=" O   LEU C 787 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 812 through 825
      removed outlier: 3.923A  pdb=" N   ARG C 824 " --> pdb=" O   SER C 820 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA C 825 " --> pdb=" O   GLN C 821 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 844 through 862
      removed outlier: 3.747A  pdb=" N   THR C 853 " --> pdb=" O   HIS C 849 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 59
      removed outlier: 3.726A  pdb=" N   HIS D  69 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 99 through 102
      removed outlier: 3.546A  pdb=" N   LEU D  99 " --> pdb=" O   LEU A 950 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 142 through 144
    Processing sheet with id=AA4, first strand: chain 'D' and resid 188 through 192
      removed outlier: 6.503A  pdb=" N   SER D 201 " --> pdb=" O   PRO D 190 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   ILE D 192 " --> pdb=" O   PHE D 199 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   PHE D 199 " --> pdb=" O   ILE D 192 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 236 through 238
    Processing sheet with id=AA6, first strand: chain 'D' and resid 236 through 238
    Processing sheet with id=AA7, first strand: chain 'D' and resid 270 through 272
      removed outlier: 6.532A  pdb=" N   GLN D 322 " --> pdb=" O   VAL D 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 286 through 290
    Processing sheet with id=AA9, first strand: chain 'D' and resid 335 through 337
    Processing sheet with id=AB1, first strand: chain 'D' and resid 350 through 356
      removed outlier: 5.738A  pdb=" N   ILE D 351 " --> pdb=" O   LEU D 368 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   LEU D 368 " --> pdb=" O   ILE D 351 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ARG D 353 " --> pdb=" O   MET D 366 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU D 375 " --> pdb=" O   GLU D 413 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLU D 413 " --> pdb=" O   LEU D 375 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   LEU D 377 " --> pdb=" O   ILE D 411 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 426 through 428
      removed outlier: 6.518A  pdb=" N   ASP D 459 " --> pdb=" O   ILE D 482 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE D 482 " --> pdb=" O   ASP D 459 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 504 through 506
    Processing sheet with id=AB4, first strand: chain 'D' and resid 546 through 551
      removed outlier: 3.513A  pdb=" N   SER D 563 " --> pdb=" O   SER D 546 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   SER D 564 " --> pdb=" O   PRO D 568 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   VAL D 571 " --> pdb=" O   MET D 594 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LYS D 575 " --> pdb=" O   PHE D 590 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   PHE D 590 " --> pdb=" O   LYS D 575 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   SER D 577 " --> pdb=" O   PRO D 588 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 613
      removed outlier: 4.561A  pdb=" N   TYR D 621 " --> pdb=" O   ASP D 677 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP D 677 " --> pdb=" O   TYR D 621 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL D 673 " --> pdb=" O   TYR D 625 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   VAL D 674 " --> pdb=" O   PRO D 637 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL D 639 " --> pdb=" O   VAL D 674 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   ILE D 676 " --> pdb=" O   VAL D 639 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   PHE D 641 " --> pdb=" O   ILE D 676 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   HIS D 636 " --> pdb=" O   ASP D 719 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   SER D 721 " --> pdb=" O   HIS D 636 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   THR D 638 " --> pdb=" O   SER D 721 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   VAL D 723 " --> pdb=" O   THR D 638 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   LEU D 640 " --> pdb=" O   VAL D 723 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ILE D 725 " --> pdb=" O   LEU D 640 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 750 through 752
      removed outlier: 6.379A  pdb=" N   ILE D 801 " --> pdb=" O   GLN D 832 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   TYR D 834 " --> pdb=" O   ILE D 801 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   HIS D 803 " --> pdb=" O   TYR D 834 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 845 through 848
      removed outlier: 4.194A  pdb=" N   GLU A 845 " --> pdb=" O   ARG A 855 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU A 853 " --> pdb=" O   VAL A 847 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 862 through 866
      removed outlier: 4.052A  pdb=" N   ARG A 955 " --> pdb=" O   VAL A 962 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 986 through 987
      removed outlier: 3.518A  pdb=" N   LEU A1040 " --> pdb=" O   ILE A 987 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1029 through 1031
      removed outlier: 4.163A  pdb=" N   ILE A 993 " --> pdb=" O   ILE A1031 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A1055 " --> pdb=" O   TYR A1078 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1060 through 1062
      removed outlier: 3.707A  pdb=" N   TRP A1100 " --> pdb=" O   LEU A1090 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP A1092 " --> pdb=" O   LEU A1098 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   LEU A1098 " --> pdb=" O   ASP A1092 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 1029 through 1031
      removed outlier: 4.133A  pdb=" N   ILE B 993 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 1060 through 1062
    Processing sheet with id=AC5, first strand: chain 'C' and resid 56 through 59
      removed outlier: 6.812A  pdb=" N   ILE C  90 " --> pdb=" O   SER C  68 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   ARG C  70 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   SER C  88 " --> pdb=" O   ARG C  70 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   TYR C  72 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU C  86 " --> pdb=" O   TYR C  72 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LEU C  74 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   SER C  84 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 142 through 144
    Processing sheet with id=AC7, first strand: chain 'C' and resid 188 through 193
      removed outlier: 6.575A  pdb=" N   SER C 201 " --> pdb=" O   PRO C 190 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   ILE C 192 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   PHE C 199 " --> pdb=" O   ILE C 192 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 236 through 238
    Processing sheet with id=AC9, first strand: chain 'C' and resid 236 through 238
    Processing sheet with id=AD1, first strand: chain 'C' and resid 270 through 272
      removed outlier: 6.551A  pdb=" N   GLN C 322 " --> pdb=" O   VAL C 330 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 286 through 290
    Processing sheet with id=AD3, first strand: chain 'C' and resid 335 through 337
    Processing sheet with id=AD4, first strand: chain 'C' and resid 350 through 356
      removed outlier: 5.459A  pdb=" N   ILE C 351 " --> pdb=" O   LEU C 368 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LEU C 368 " --> pdb=" O   ILE C 351 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ARG C 353 " --> pdb=" O   MET C 366 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 426 through 428
      removed outlier: 6.759A  pdb=" N   ARG C 455 " --> pdb=" O   GLU C 485 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLU C 485 " --> pdb=" O   ARG C 455 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   THR C 457 " --> pdb=" O   LYS C 483 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 504 through 506
    Processing sheet with id=AD7, first strand: chain 'C' and resid 546 through 551
      removed outlier: 3.643A  pdb=" N   HIS C 561 " --> pdb=" O   SER C 548 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL C 559 " --> pdb=" O   SER C 550 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   SER C 564 " --> pdb=" O   PRO C 568 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   VAL C 571 " --> pdb=" O   SER C 593 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   SER C 593 " --> pdb=" O   VAL C 571 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   VAL C 573 " --> pdb=" O   TRP C 591 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN C 587 " --> pdb=" O   SER C 577 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 608 through 613
      removed outlier: 4.175A  pdb=" N   TYR C 621 " --> pdb=" O   ASP C 677 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL C 673 " --> pdb=" O   TYR C 625 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   VAL C 674 " --> pdb=" O   PRO C 637 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL C 639 " --> pdb=" O   VAL C 674 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ILE C 676 " --> pdb=" O   VAL C 639 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   PHE C 641 " --> pdb=" O   ILE C 676 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   HIS C 636 " --> pdb=" O   ASP C 719 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   SER C 721 " --> pdb=" O   HIS C 636 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   THR C 638 " --> pdb=" O   SER C 721 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   VAL C 723 " --> pdb=" O   THR C 638 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   LEU C 640 " --> pdb=" O   VAL C 723 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   ILE C 725 " --> pdb=" O   LEU C 640 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   ILE C 750 " --> pdb=" O   VAL C 723 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE C 725 " --> pdb=" O   ILE C 750 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   GLY C 752 " --> pdb=" O   ILE C 725 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLY C 727 " --> pdb=" O   GLY C 752 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ALA C 749 " --> pdb=" O   LEU C 800 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   LEU C 802 " --> pdb=" O   ALA C 749 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ALA C 751 " --> pdb=" O   LEU C 802 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   GLY C 804 " --> pdb=" O   ALA C 751 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   GLN C 832 " --> pdb=" O   LEU C 799 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ILE C 801 " --> pdb=" O   GLN C 832 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   TYR C 834 " --> pdb=" O   ILE C 801 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   HIS C 803 " --> pdb=" O   TYR C 834 " (cutoff:3.500A)

    520 hydrogen bonds defined for protein.
    1347 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.84

  Time building geometry restraints manager: 6.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3858
        1.33 -     1.45: 3786
        1.45 -     1.57: 9339
        1.57 -     1.69: 0
        1.69 -     1.81: 117
  Bond restraints: 17100
  Sorted by residual:
  bond pdb=" N   CYS C 600 "
       pdb=" CA  CYS C 600 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 9.10e-03 1.21e+04 1.86e+01
  bond pdb=" C   THR C 567 "
       pdb=" N   PRO C 568 "
    ideal  model  delta    sigma   weight residual
    1.329  1.371 -0.042 1.18e-02 7.18e+03 1.27e+01
  bond pdb=" N   ILE A1082 "
       pdb=" CA  ILE A1082 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.07e-02 8.73e+03 1.03e+01
  bond pdb=" N   ASP D 603 "
       pdb=" CA  ASP D 603 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 9.10e-03 1.21e+04 9.95e+00
  bond pdb=" C   CYS C 600 "
       pdb=" O   CYS C 600 "
    ideal  model  delta    sigma   weight residual
    1.233  1.248 -0.015 4.80e-03 4.34e+04 9.61e+00
  ... (remaining 17095 not shown)

  Histogram of bond angle deviations from ideal:
       99.09 -   106.14: 566
      106.14 -   113.20: 9066
      113.20 -   120.26: 6293
      120.26 -   127.32: 7025
      127.32 -   134.38: 273
  Bond angle restraints: 23223
  Sorted by residual:
  angle pdb=" N   PRO C 601 "
        pdb=" CA  PRO C 601 "
        pdb=" C   PRO C 601 "
      ideal   model   delta    sigma   weight residual
     110.70  126.03  -15.33 1.22e+00 6.72e-01 1.58e+02
  angle pdb=" N   PRO D 601 "
        pdb=" CA  PRO D 601 "
        pdb=" C   PRO D 601 "
      ideal   model   delta    sigma   weight residual
     110.70  125.22  -14.52 1.22e+00 6.72e-01 1.42e+02
  angle pdb=" N   ILE A1082 "
        pdb=" CA  ILE A1082 "
        pdb=" C   ILE A1082 "
      ideal   model   delta    sigma   weight residual
     113.10  105.42    7.68 9.70e-01 1.06e+00 6.27e+01
  angle pdb=" N   PRO C 602 "
        pdb=" CA  PRO C 602 "
        pdb=" C   PRO C 602 "
      ideal   model   delta    sigma   weight residual
     112.47  124.58  -12.11 2.06e+00 2.36e-01 3.46e+01
  angle pdb=" N   VAL A 981 "
        pdb=" CA  VAL A 981 "
        pdb=" C   VAL A 981 "
      ideal   model   delta    sigma   weight residual
     113.71  108.53    5.18 9.50e-01 1.11e+00 2.97e+01
  ... (remaining 23218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 9010
       15.94 -    31.89: 901
       31.89 -    47.83: 170
       47.83 -    63.78: 39
       63.78 -    79.72: 17
  Dihedral angle restraints: 10137
    sinusoidal: 4141
      harmonic: 5996
  Sorted by residual:
  dihedral pdb=" CA  ALA C 154 "
           pdb=" C   ALA C 154 "
           pdb=" N   SER C 155 "
           pdb=" CA  SER C 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.72   29.28     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  SER C 729 "
           pdb=" C   SER C 729 "
           pdb=" N   TYR C 730 "
           pdb=" CA  TYR C 730 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.81   25.19     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  VAL C 772 "
           pdb=" C   VAL C 772 "
           pdb=" N   PRO C 773 "
           pdb=" CA  PRO C 773 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.19  -23.81     0      5.00e+00 4.00e-02 2.27e+01
  ... (remaining 10134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 2386
       0.111 -    0.222: 69
       0.222 -    0.334: 9
       0.334 -    0.445: 2
       0.445 -    0.556: 2
  Chirality restraints: 2468
  Sorted by residual:
  chirality pdb=" CA  PRO C 601 "
            pdb=" N   PRO C 601 "
            pdb=" C   PRO C 601 "
            pdb=" CB  PRO C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.16    0.56 2.00e-01 2.50e+01 7.73e+00
  chirality pdb=" CA  PRO D 601 "
            pdb=" N   PRO D 601 "
            pdb=" C   PRO D 601 "
            pdb=" CB  PRO D 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.23    0.49 2.00e-01 2.50e+01 6.07e+00
  chirality pdb=" CA  LEU A1057 "
            pdb=" N   LEU A1057 "
            pdb=" C   LEU A1057 "
            pdb=" CB  LEU A1057 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 2465 not shown)

  Planarity restraints: 3007
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 599 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.04e+00
        pdb=" C   SER D 599 "    0.052 2.00e-02 2.50e+03
        pdb=" O   SER D 599 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   CYS D 600 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1077 "   -0.015 2.00e-02 2.50e+03   2.94e-02 8.62e+00
        pdb=" C   ILE A1077 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ILE A1077 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TYR A1078 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1056 "    0.014 2.00e-02 2.50e+03   2.72e-02 7.42e+00
        pdb=" C   ILE A1056 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ILE A1056 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU A1057 "    0.016 2.00e-02 2.50e+03
  ... (remaining 3004 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1593
        2.74 -     3.28: 15985
        3.28 -     3.82: 26760
        3.82 -     4.36: 33296
        4.36 -     4.90: 56843
  Nonbonded interactions: 134477
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG D 251 "
            pdb=" O   ILE D 351 "
     model   vdw
     2.202 2.520
  nonbonded pdb=" NH1 ARG C 219 "
            pdb=" OG  SER C 332 "
     model   vdw
     2.227 2.520
  nonbonded pdb=" OG  SER A 989 "
            pdb=" O   VAL A1009 "
     model   vdw
     2.228 2.440
  nonbonded pdb=" O   ARG D 306 "
            pdb=" OG  SER D 309 "
     model   vdw
     2.245 2.440
  nonbonded pdb=" OH  TYR C  72 "
            pdb=" OD2 ASP C 163 "
     model   vdw
     2.249 2.440
  ... (remaining 134472 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and (resid 21 through 44 or resid 50 through 62 or resid 65 through 1 \ 
15 or resid 136 through 227 or resid 231 through 862))
}

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: 4
    Type Number    sf(0)   Gaussians
     S      79      5.16       5
     C   10687      2.51       5
     N    2832      2.21       5
     O    3015      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=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:          4.590
  Check model and map are aligned:         0.250
  Convert atoms to be neutral:             0.150
  Process input model:                     44.590
  Find NCS groups from input model:        0.880
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Set scattering table:                    0.020
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
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      :  0.005   0.042  17100  Z= 0.324
  Angle     :  0.732  15.334  23223  Z= 0.468
  Chirality :  0.053   0.556   2468
  Planarity :  0.004   0.038   3007
  Dihedral  : 13.491  79.722   6277
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.94 %
    Favored  : 93.91 %
  Rotamer Outliers :  0.60 %
  Cbeta Deviations :  0.05 %
  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: -3.70 (0.16), residues: 2037
  helix: -3.08 (0.20), residues: 319
  sheet: -2.21 (0.19), residues: 636
  loop : -2.39 (0.17), residues: 1082

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 2.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 2
  residues processed: 185
  average time/residue: 0.3412
  time to fit residues: 91.9678
Evaluate side-chains
  117 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 1.972 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1446
  time to fit residues: 3.2666
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 171 optimal weight:    1.9990
   chunk 153 optimal weight:    0.4980
   chunk 85 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 159 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 96 optimal weight:    6.9990
   chunk 118 optimal weight:    5.9990
   chunk 184 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
D  59 GLN
D  69 HIS
D 117 HIS
D 160 HIS
D 204 ASN
D 311 ASN
D 506 ASN
D 515 GLN
D 547 HIS
** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 585 HIS
D 647 GLN
D 649 GLN
D 803 HIS
** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 836 ASN
D 859 GLN
A 852 ASN
** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 HIS
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 167 ASN
C 311 ASN
C 339 GLN
C 506 ASN
C 803 HIS

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.086  17100  Z= 0.203
  Angle     :  0.592  15.141  23223  Z= 0.306
  Chirality :  0.045   0.243   2468
  Planarity :  0.005   0.067   3007
  Dihedral  :  5.068  31.044   2236
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.45 %
    Favored  : 94.50 %
  Rotamer Outliers :  1.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.74 %
    Twisted General : 0.05 %

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: -2.72 (0.17), residues: 2037
  helix: -1.41 (0.26), residues: 322
  sheet: -1.72 (0.19), residues: 632
  loop : -1.95 (0.17), residues: 1083

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 2.142 
Fit side-chains
  outliers start: 23
  outliers final: 13
  residues processed: 134
  average time/residue: 0.3065
  time to fit residues: 62.3219
Evaluate side-chains
  124 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 2.024 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1569
  time to fit residues: 6.3860
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 153 optimal weight:    4.9990
   chunk 125 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0170
   chunk 184 optimal weight:    5.9990
   chunk 199 optimal weight:    3.9990
   chunk 164 optimal weight:    8.9990
   chunk 183 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 148 optimal weight:    2.9990
   overall best weight:    1.9824

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

Flipped N/Q/H residues before XYZ refinement:
** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 983 HIS
B1072 GLN
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 515 GLN
C 547 HIS
C 839 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.090  17100  Z= 0.259
  Angle     :  0.581  14.667  23223  Z= 0.300
  Chirality :  0.044   0.213   2468
  Planarity :  0.004   0.071   3007
  Dihedral  :  4.975  30.804   2236
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.69 %
    Favored  : 94.21 %
  Rotamer Outliers :  1.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.74 %
    Twisted General : 0.05 %

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: -2.27 (0.18), residues: 2037
  helix: -0.85 (0.28), residues: 323
  sheet: -1.44 (0.20), residues: 645
  loop : -1.72 (0.18), residues: 1069

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 1.849 
Fit side-chains
   revert: symmetry clash
  outliers start: 20
  outliers final: 10
  residues processed: 137
  average time/residue: 0.2903
  time to fit residues: 62.3281
Evaluate side-chains
  124 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 1.931 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1534
  time to fit residues: 5.3844
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 182 optimal weight:    0.9980
   chunk 138 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 185 optimal weight:    6.9990
   chunk 196 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 175 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
D 339 GLN
** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 929 GLN
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.094  17100  Z= 0.306
  Angle     :  0.588  13.710  23223  Z= 0.303
  Chirality :  0.045   0.188   2468
  Planarity :  0.004   0.070   3007
  Dihedral  :  5.017  30.505   2236
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.65 %
    Favored  : 94.26 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.74 %
    Twisted General : 0.05 %

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: -2.02 (0.18), residues: 2037
  helix: -0.59 (0.28), residues: 324
  sheet: -1.31 (0.20), residues: 648
  loop : -1.55 (0.18), residues: 1065

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.839 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 15
  residues processed: 139
  average time/residue: 0.2778
  time to fit residues: 60.0753
Evaluate side-chains
  130 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 2.102 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.1588
  time to fit residues: 7.1327
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 163 optimal weight:    4.9990
   chunk 111 optimal weight:    0.0870
   chunk 2 optimal weight:    4.9990
   chunk 146 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 167 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 100 optimal weight:    0.5980
   chunk 176 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.7364

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

Flipped N/Q/H residues before XYZ refinement:
** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 929 GLN
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
C 664 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.051  17100  Z= 0.227
  Angle     :  0.564  14.451  23223  Z= 0.290
  Chirality :  0.044   0.244   2468
  Planarity :  0.004   0.067   3007
  Dihedral  :  4.912  30.857   2236
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.84 %
    Favored  : 94.06 %
  Rotamer Outliers :  1.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.78 (0.18), residues: 2037
  helix: -0.31 (0.29), residues: 323
  sheet: -1.14 (0.20), residues: 648
  loop : -1.44 (0.19), residues: 1066

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 2.008 
Fit side-chains
   revert: symmetry clash
  outliers start: 25
  outliers final: 9
  residues processed: 144
  average time/residue: 0.3046
  time to fit residues: 68.1417
Evaluate side-chains
  124 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 2.143 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1804
  time to fit residues: 5.9100
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 176 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 115 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   chunk 196 optimal weight:    0.6980
   chunk 163 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9990
   chunk 103 optimal weight:    0.2980
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
C 849 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.237  17100  Z= 0.241
  Angle     :  0.588  17.349  23223  Z= 0.303
  Chirality :  0.043   0.186   2468
  Planarity :  0.004   0.072   3007
  Dihedral  :  4.681  31.196   2236
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.35 %
    Favored  : 94.60 %
  Rotamer Outliers :  0.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.74 %
    Twisted General : 0.05 %

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: -1.49 (0.18), residues: 2037
  helix:  0.00 (0.30), residues: 324
  sheet: -0.92 (0.20), residues: 655
  loop : -1.30 (0.19), residues: 1058

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 2.022 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 134
  average time/residue: 0.2984
  time to fit residues: 61.7344
Evaluate side-chains
  124 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 2.141 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.2287
  time to fit residues: 5.9927
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 189 optimal weight:    8.9990
   chunk 22 optimal weight:    0.6980
   chunk 111 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9990
   chunk 165 optimal weight:    6.9990
   chunk 109 optimal weight:    0.6980
   chunk 195 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 121 optimal weight:    0.1980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 704 GLN
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
C 695 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.068  17100  Z= 0.215
  Angle     :  0.580  16.228  23223  Z= 0.294
  Chirality :  0.044   0.317   2468
  Planarity :  0.004   0.077   3007
  Dihedral  :  4.671  30.725   2236
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.65 %
    Favored  : 94.31 %
  Rotamer Outliers :  0.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.36 (0.18), residues: 2037
  helix:  0.15 (0.30), residues: 322
  sheet: -0.81 (0.20), residues: 643
  loop : -1.25 (0.18), residues: 1072

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 2.060 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 4
  residues processed: 124
  average time/residue: 0.3016
  time to fit residues: 58.5690
Evaluate side-chains
  110 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 1.988 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1534
  time to fit residues: 3.8634
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 116 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 133 optimal weight:   10.0000
   chunk 96 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 153 optimal weight:    0.2980
   chunk 177 optimal weight:    0.4980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.253  17100  Z= 0.262
  Angle     :  0.577  16.062  23223  Z= 0.295
  Chirality :  0.044   0.299   2468
  Planarity :  0.004   0.066   3007
  Dihedral  :  4.597  30.935   2236
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.35 %
    Favored  : 94.60 %
  Rotamer Outliers :  0.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.23 (0.18), residues: 2037
  helix:  0.29 (0.30), residues: 323
  sheet: -0.72 (0.20), residues: 654
  loop : -1.18 (0.19), residues: 1060

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 2.109 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 117
  average time/residue: 0.3081
  time to fit residues: 55.3325
Evaluate side-chains
  112 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 2.079 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1662
  time to fit residues: 4.2785
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 187 optimal weight:    8.9990
   chunk 171 optimal weight:    2.9990
   chunk 182 optimal weight:    4.9990
   chunk 109 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 164 optimal weight:    0.0670
   chunk 172 optimal weight:    0.0770
   chunk 181 optimal weight:    2.9990
   chunk 119 optimal weight:    0.6980
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.102  17100  Z= 0.162
  Angle     :  0.552  15.466  23223  Z= 0.279
  Chirality :  0.043   0.188   2468
  Planarity :  0.004   0.095   3007
  Dihedral  :  4.436  31.024   2236
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.96 %
    Favored  : 94.99 %
  Rotamer Outliers :  0.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.01 (0.19), residues: 2037
  helix:  0.52 (0.30), residues: 323
  sheet: -0.49 (0.21), residues: 634
  loop : -1.12 (0.18), residues: 1080

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 1.799 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 131
  average time/residue: 0.3050
  time to fit residues: 62.0319
Evaluate side-chains
  111 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 1.969 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1516
  time to fit residues: 3.5834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 192 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 134 optimal weight:    0.3980
   chunk 202 optimal weight:    2.9990
   chunk 186 optimal weight:    3.9990
   chunk 161 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 124 optimal weight:    2.9990
   chunk 98 optimal weight:    0.2980
   chunk 127 optimal weight:    8.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 ASN
C 744 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.142  17100  Z= 0.217
  Angle     :  0.578  15.746  23223  Z= 0.293
  Chirality :  0.043   0.182   2468
  Planarity :  0.005   0.142   3007
  Dihedral  :  4.511  30.859   2236
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.35 %
    Favored  : 94.60 %
  Rotamer Outliers :  0.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -0.98 (0.19), residues: 2037
  helix:  0.53 (0.30), residues: 324
  sheet: -0.39 (0.21), residues: 637
  loop : -1.16 (0.18), residues: 1076

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 2.148 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 112
  average time/residue: 0.3023
  time to fit residues: 53.1750
Evaluate side-chains
  107 residues out of total 1823 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 1.980 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1447
  time to fit residues: 3.2404
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 171 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 148 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 161 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 165 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 141 optimal weight:    0.0570
   overall best weight:    1.9904

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

Flipped N/Q/H residues before XYZ refinement:
** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.083359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.066358 restraints weight = 42330.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 3.07
r_work: 0.3116 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work: 0.3095 rms_B_bonded: 2.83 restraints_weight: 0.1250
r_work: 0.3084 rms_B_bonded: 2.88 restraints_weight: 0.0625
r_work: 0.3072 rms_B_bonded: 2.97 restraints_weight: 0.0312
r_work: 0.3060 rms_B_bonded: 3.08 restraints_weight: 0.0156
r_work: 0.3047 rms_B_bonded: 3.22 restraints_weight: 0.0078
r_work: 0.3034 rms_B_bonded: 3.38 restraints_weight: 0.0039
r_work: 0.3020 rms_B_bonded: 3.57 restraints_weight: 0.0020
r_work: 0.3006 rms_B_bonded: 3.79 restraints_weight: 0.0010
r_work: 0.2990 rms_B_bonded: 4.04 restraints_weight: 0.0005
r_work: 0.2974 rms_B_bonded: 4.32 restraints_weight: 0.0002
r_work: 0.2957 rms_B_bonded: 4.64 restraints_weight: 0.0001
r_work: 0.2939 rms_B_bonded: 4.99 restraints_weight: 0.0001
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.114  17100  Z= 0.255
  Angle     :  0.582  15.709  23223  Z= 0.296
  Chirality :  0.044   0.181   2468
  Planarity :  0.005   0.124   3007
  Dihedral  :  4.643  30.537   2236
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.74 %
    Favored  : 94.21 %
  Rotamer Outliers :  0.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -0.99 (0.19), residues: 2037
  helix:  0.47 (0.30), residues: 324
  sheet: -0.40 (0.21), residues: 642
  loop : -1.14 (0.19), residues: 1071

===============================================================================
Job complete
usr+sys time: 2805.00 seconds
wall clock time: 52 minutes 38.61 seconds (3158.61 seconds total)