Starting phenix.real_space_refine
on Sun Dec 10 04:23:25 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/12_2023/7yp7_33995.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/12_2023/7yp7_33995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/12_2023/7yp7_33995.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/12_2023/7yp7_33995.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/12_2023/7yp7_33995.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp7_33995/12_2023/7yp7_33995.pdb"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5515 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5038      2.51       5
     N    1371      2.21       5
     O    1452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  273": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  309": "OE1" <-> "OE2"
    Residue "A GLU  330": "OE1" <-> "OE2"
    Residue "A GLU  344": "OE1" <-> "OE2"
    Residue "A PHE  345": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  392": "OE1" <-> "OE2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "B ARG  129": "NH1" <-> "NH2"
    Residue "B GLU  130": "OE1" <-> "OE2"
    Residue "B PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   22": "OE1" <-> "OE2"
    Residue "N ARG   98": "NH1" <-> "NH2"
    Residue "R GLU  876": "OE1" <-> "OE2"
    Residue "R ARG  879": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7909
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1859
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2616
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2017
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 242}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 4.77, per 1000 atoms: 0.60
  Number of scatterers: 7909
  At special positions: 0
  Unit cell: (92.88, 99.36, 131.76, 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      48     16.00
     O    1452      8.00
     N    1371      7.00
     C    5038      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 686 " - pdb=" SG  CYS R 770 " distance=2.03

  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 10 sheets defined
      32.5% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 38
      removed outlier: 3.680A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ILE A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.647A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 343
      removed outlier: 3.742A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 371
    Processing helix  chain 'A' and resid 372 through 391
      removed outlier: 3.581A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.591A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.565A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
      removed outlier: 3.908A  pdb=" N   ALA G  10 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.616A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   CYS G  41 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 622 through 644
      removed outlier: 4.193A  pdb=" N   ILE R 633 " --> pdb=" O   GLY R 629 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE R 634 " --> pdb=" O   LEU R 630 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER R 636 " --> pdb=" O   SER R 632 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR R 641 " --> pdb=" O   VAL R 637 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR R 642 " --> pdb=" O   THR R 638 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 651 through 674
      removed outlier: 3.629A  pdb=" N   LEU R 657 " --> pdb=" O   PRO R 653 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE R 658 " --> pdb=" O   SER R 654 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LEU R 672 " --> pdb=" O   ASN R 668 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU R 673 " --> pdb=" O   LEU R 669 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 683 through 716
      removed outlier: 3.660A  pdb=" N   VAL R 689 " --> pdb=" O   PHE R 685 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL R 691 " --> pdb=" O   ILE R 687 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   HIS R 694 " --> pdb=" O   ALA R 690 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   PHE R 696 " --> pdb=" O   PHE R 692 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER R 700 " --> pdb=" O   PHE R 696 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET R 704 " --> pdb=" O   SER R 700 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU R 706 " --> pdb=" O   THR R 702 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE R 709 " --> pdb=" O   GLY R 705 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR R 712 " --> pdb=" O   ALA R 708 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 726 through 735
      removed outlier: 3.737A  pdb=" N   VAL R 733 " --> pdb=" O   LYS R 729 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 737 through 748
      removed outlier: 4.542A  pdb=" N   SER R 743 " --> pdb=" O   ALA R 739 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE R 744 " --> pdb=" O   VAL R 740 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL R 745 " --> pdb=" O   VAL R 741 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE R 748 " --> pdb=" O   ILE R 744 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 775 through 782
      removed outlier: 3.513A  pdb=" N   TYR R 779 " --> pdb=" O   ASN R 775 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE R 780 " --> pdb=" O   VAL R 776 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 782 through 791
      removed outlier: 3.895A  pdb=" N   ILE R 789 " --> pdb=" O   TYR R 785 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 794 through 808
      removed outlier: 3.763A  pdb=" N   VAL R 800 " --> pdb=" O   MET R 796 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU R 801 " --> pdb=" O   PHE R 797 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE R 807 " --> pdb=" O   GLN R 803 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 823 through 834
      removed outlier: 3.533A  pdb=" N   GLY R 829 " --> pdb=" O   ARG R 825 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR R 831 " --> pdb=" O   ILE R 827 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   PHE R 832 " --> pdb=" O   ALA R 828 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 835 through 838
      removed outlier: 3.935A  pdb=" N   TRP R 838 " --> pdb=" O   GLY R 835 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 835 through 838'
    Processing helix  chain 'R' and resid 839 through 845
      removed outlier: 3.901A  pdb=" N   PHE R 843 " --> pdb=" O   GLY R 839 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 851 through 860
      removed outlier: 3.565A  pdb=" N   ASN R 860 " --> pdb=" O   PHE R 856 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 862 through 872
    Processing helix  chain 'R' and resid 875 through 883
      removed outlier: 4.348A  pdb=" N   GLN R 881 " --> pdb=" O   ASN R 877 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TRP R 882 " --> pdb=" O   VAL R 878 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG R 883 " --> pdb=" O   ARG R 879 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 3.655A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.335A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.568A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.788A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASP B  83 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.923A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.622A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.159A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.557A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.100A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.535A  pdb=" N   LEU N  81 " --> pdb=" O   LEU N  20 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.568A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ALA N  40 " --> pdb=" O   GLY N  44 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLY N  44 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    272 hydrogen bonds defined for protein.
    780 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: 2.25

  Time building geometry restraints manager: 2.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2550
        1.34 -     1.46: 1861
        1.46 -     1.58: 3598
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 8074
  Sorted by residual:
  bond pdb=" N   VAL R 848 "
       pdb=" CA  VAL R 848 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.10e+01
  bond pdb=" N   LYS A 280 "
       pdb=" CA  LYS A 280 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.19e+00
  bond pdb=" N   ILE A 276 "
       pdb=" CA  ILE A 276 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.19e-02 7.06e+03 7.96e+00
  bond pdb=" N   VAL N 110 "
       pdb=" CA  VAL N 110 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.20e-02 6.94e+03 7.95e+00
  bond pdb=" N   VAL R 850 "
       pdb=" CA  VAL R 850 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.67e+00
  ... (remaining 8069 not shown)

  Histogram of bond angle deviations from ideal:
       99.65 -   106.60: 156
      106.60 -   113.55: 4375
      113.55 -   120.50: 3328
      120.50 -   127.45: 3003
      127.45 -   134.40: 79
  Bond angle restraints: 10941
  Sorted by residual:
  angle pdb=" N   ARG R 650 "
        pdb=" CA  ARG R 650 "
        pdb=" C   ARG R 650 "
      ideal   model   delta    sigma   weight residual
     112.45  124.54  -12.09 1.39e+00 5.18e-01 7.56e+01
  angle pdb=" N   TRP R 838 "
        pdb=" CA  TRP R 838 "
        pdb=" C   TRP R 838 "
      ideal   model   delta    sigma   weight residual
     113.16  105.61    7.55 1.24e+00 6.50e-01 3.71e+01
  angle pdb=" C   GLY R 846 "
        pdb=" N   PRO R 847 "
        pdb=" CA  PRO R 847 "
      ideal   model   delta    sigma   weight residual
     119.84  126.67   -6.83 1.25e+00 6.40e-01 2.98e+01
  angle pdb=" C   ILE B 171 "
        pdb=" N   GLU B 172 "
        pdb=" CA  GLU B 172 "
      ideal   model   delta    sigma   weight residual
     121.54  131.56  -10.02 1.91e+00 2.74e-01 2.75e+01
  angle pdb=" N   ILE A 372 "
        pdb=" CA  ILE A 372 "
        pdb=" C   ILE A 372 "
      ideal   model   delta    sigma   weight residual
     113.22  107.01    6.21 1.23e+00 6.61e-01 2.55e+01
  ... (remaining 10936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 4243
       17.63 -    35.26: 416
       35.26 -    52.88: 76
       52.88 -    70.51: 16
       70.51 -    88.14: 12
  Dihedral angle restraints: 4763
    sinusoidal: 1839
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" CA  GLN R 822 "
           pdb=" C   GLN R 822 "
           pdb=" N   ASP R 823 "
           pdb=" CA  ASP R 823 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.18   28.82     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  CYS B 204 "
           pdb=" C   CYS B 204 "
           pdb=" N   ASP B 205 "
           pdb=" CA  ASP B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.89   26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CB  CYS R 686 "
           pdb=" SG  CYS R 686 "
           pdb=" SG  CYS R 770 "
           pdb=" CB  CYS R 770 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.11   42.11     1      1.00e+01 1.00e-02 2.48e+01
  ... (remaining 4760 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1145
       0.108 -    0.217: 81
       0.217 -    0.325: 2
       0.325 -    0.433: 0
       0.433 -    0.541: 1
  Chirality restraints: 1229
  Sorted by residual:
  chirality pdb=" CA  ARG R 650 "
            pdb=" N   ARG R 650 "
            pdb=" C   ARG R 650 "
            pdb=" CB  ARG R 650 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.33e+00
  chirality pdb=" CA  TYR R 652 "
            pdb=" N   TYR R 652 "
            pdb=" C   TYR R 652 "
            pdb=" CB  TYR R 652 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  PRO R 847 "
            pdb=" N   PRO R 847 "
            pdb=" C   PRO R 847 "
            pdb=" CB  PRO R 847 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1226 not shown)

  Planarity restraints: 1397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.060 5.00e-02 4.00e+02   9.17e-02 1.35e+01
        pdb=" N   PRO B 236 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 837 "    0.013 2.00e-02 2.50e+03   2.79e-02 7.79e+00
        pdb=" C   THR R 837 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR R 837 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP R 838 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 737 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO R 738 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO R 738 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 738 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1394 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.44: 29
        2.44 -     3.05: 4409
        3.05 -     3.67: 11444
        3.67 -     4.28: 16896
        4.28 -     4.90: 28510
  Nonbonded interactions: 61288
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 213 "
            pdb=" OD1 ASN A 218 "
     model   vdw
     1.823 2.520
  nonbonded pdb=" CG  GLN A 213 "
            pdb=" OD1 ASN A 218 "
     model   vdw
     2.084 3.440
  nonbonded pdb=" CD  GLN A 213 "
            pdb=" OD1 ASN A 218 "
     model   vdw
     2.224 3.270
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.254 2.440
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" CG2 ILE A 348 "
     model   vdw
     2.316 3.460
  ... (remaining 61283 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
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 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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.220
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     24.760
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
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      :  0.007   0.064   8074  Z= 0.442
  Angle     :  0.950  12.086  10941  Z= 0.584
  Chirality :  0.059   0.541   1229
  Planarity :  0.006   0.092   1397
  Dihedral  : 15.192  88.139   2867
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  7.68 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  6.83 %
    Favored  : 91.73 %
  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: -4.81 (0.21), residues: 989
  helix: -4.72 (0.10), residues: 316
  sheet: -1.51 (0.32), residues: 223
  loop : -2.79 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.037   0.003   TRP R 771 
   HIS   0.011   0.002   HIS A 357 
   PHE   0.026   0.002   PHE R 730 
   TYR   0.025   0.002   TYR B  59 
   ARG   0.006   0.001   ARG A 389 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 180
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 7
  residues processed: 191
  average time/residue: 0.2777
  time to fit residues: 66.4394
Evaluate side-chains
  154 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 147
  time to evaluate  : 0.936 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 1
  residues processed: 7
  average time/residue: 0.2016
  time to fit residues: 3.0968
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    0.1980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 218 ASN
A 227 GLN
B   9 GLN
B  13 GLN
B 183 HIS
B 230 ASN
B 239 ASN
G  24 ASN
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
N  31 ASN
R 860 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8074  Z= 0.185
  Angle     :  0.564   6.298  10941  Z= 0.313
  Chirality :  0.042   0.175   1229
  Planarity :  0.005   0.069   1397
  Dihedral  :  5.315  20.868   1097
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.16 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.95 %
    Favored  : 85.61 %
  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: -3.25 (0.24), residues: 989
  helix: -2.48 (0.23), residues: 321
  sheet: -1.22 (0.33), residues: 226
  loop : -2.30 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 234 
   HIS   0.003   0.001   HIS A 220 
   PHE   0.011   0.001   PHE R 856 
   TYR   0.014   0.001   TYR R 785 
   ARG   0.006   0.000   ARG B 256 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 196
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 6
  residues processed: 202
  average time/residue: 0.2577
  time to fit residues: 66.2149
Evaluate side-chains
  154 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 148
  time to evaluate  : 0.918 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0732
  time to fit residues: 1.9951
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
B 259 GLN
B 340 ASN
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 710 HIS
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8074  Z= 0.181
  Angle     :  0.532   6.889  10941  Z= 0.290
  Chirality :  0.042   0.181   1229
  Planarity :  0.004   0.065   1397
  Dihedral  :  4.854  20.041   1097
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.46 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.27 %
    Favored  : 81.53 %
  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: -2.33 (0.26), residues: 989
  helix: -1.22 (0.28), residues: 320
  sheet: -0.96 (0.33), residues: 234
  loop : -2.04 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 234 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.009   0.001   PHE R 730 
   TYR   0.010   0.001   TYR R 722 
   ARG   0.005   0.000   ARG B 256 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 7
  residues processed: 169
  average time/residue: 0.2322
  time to fit residues: 50.9565
Evaluate side-chains
  157 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.875 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0731
  time to fit residues: 2.0774
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 67 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0030
   chunk 84 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  88 ASN
B 340 ASN
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 863 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8074  Z= 0.152
  Angle     :  0.509   6.151  10941  Z= 0.275
  Chirality :  0.041   0.179   1229
  Planarity :  0.004   0.063   1397
  Dihedral  :  4.573  18.738   1097
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.85 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 18.71 %
    Favored  : 80.10 %
  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: -1.84 (0.26), residues: 989
  helix: -0.57 (0.29), residues: 320
  sheet: -0.72 (0.34), residues: 229
  loop : -1.95 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 234 
   HIS   0.003   0.001   HIS R 694 
   PHE   0.010   0.001   PHE R 622 
   TYR   0.011   0.001   TYR R 625 
   ARG   0.004   0.000   ARG B 256 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 167
  average time/residue: 0.2226
  time to fit residues: 49.1820
Evaluate side-chains
  155 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 0.900 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0869
  time to fit residues: 1.9143
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0270
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8074  Z= 0.156
  Angle     :  0.506   7.239  10941  Z= 0.272
  Chirality :  0.041   0.178   1229
  Planarity :  0.003   0.062   1397
  Dihedral  :  4.483  22.619   1097
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.16 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 19.54 %
    Favored  : 78.90 %
  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: -1.50 (0.27), residues: 989
  helix: -0.13 (0.30), residues: 320
  sheet: -0.65 (0.34), residues: 230
  loop : -1.79 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 234 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.008   0.001   PHE B 241 
   TYR   0.010   0.001   TYR R 625 
   ARG   0.003   0.000   ARG B 256 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 10
  residues processed: 164
  average time/residue: 0.2332
  time to fit residues: 49.9671
Evaluate side-chains
  158 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.900 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0754
  time to fit residues: 2.5919
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8074  Z= 0.255
  Angle     :  0.584   9.551  10941  Z= 0.310
  Chirality :  0.043   0.142   1229
  Planarity :  0.005   0.090   1397
  Dihedral  :  4.808  19.275   1097
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.07 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.38 %
    Favored  : 77.94 %
  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: -1.46 (0.27), residues: 989
  helix:  0.06 (0.30), residues: 312
  sheet: -0.73 (0.33), residues: 236
  loop : -1.82 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP A 234 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.011   0.001   PHE B 241 
   TYR   0.012   0.001   TYR B 105 
   ARG   0.010   0.000   ARG R 825 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 11
  residues processed: 159
  average time/residue: 0.2513
  time to fit residues: 51.3409
Evaluate side-chains
  157 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.865 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1151
  time to fit residues: 3.1590
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 94 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8074  Z= 0.264
  Angle     :  0.596   8.762  10941  Z= 0.314
  Chirality :  0.043   0.167   1229
  Planarity :  0.005   0.085   1397
  Dihedral  :  4.861  19.566   1097
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.27 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 20.74 %
    Favored  : 77.34 %
  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: -1.38 (0.27), residues: 989
  helix:  0.13 (0.30), residues: 315
  sheet: -0.71 (0.33), residues: 234
  loop : -1.77 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP A 234 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.010   0.001   PHE B 241 
   TYR   0.016   0.001   TYR B 105 
   ARG   0.012   0.001   ARG A 283 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 14
  residues processed: 156
  average time/residue: 0.2422
  time to fit residues: 49.0081
Evaluate side-chains
  161 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.966 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0765
  time to fit residues: 3.2531
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0000
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0000
   chunk 74 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8074  Z= 0.150
  Angle     :  0.546   8.904  10941  Z= 0.286
  Chirality :  0.041   0.149   1229
  Planarity :  0.005   0.084   1397
  Dihedral  :  4.494  18.209   1097
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.17 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 20.86 %
    Favored  : 78.66 %
  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: -1.24 (0.27), residues: 989
  helix:  0.19 (0.30), residues: 327
  sheet: -0.58 (0.34), residues: 230
  loop : -1.72 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 234 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.008   0.001   PHE B 241 
   TYR   0.010   0.001   TYR R 625 
   ARG   0.012   0.000   ARG R 825 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 156
  average time/residue: 0.2507
  time to fit residues: 50.4026
Evaluate side-chains
  151 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 0.917 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0798
  time to fit residues: 1.6345
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8074  Z= 0.189
  Angle     :  0.571   9.072  10941  Z= 0.298
  Chirality :  0.042   0.196   1229
  Planarity :  0.004   0.080   1397
  Dihedral  :  4.537  17.932   1097
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.97 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 22.42 %
    Favored  : 77.10 %
  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: -1.14 (0.27), residues: 989
  helix:  0.24 (0.30), residues: 327
  sheet: -0.45 (0.34), residues: 226
  loop : -1.68 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 234 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.011   0.001   PHE B 234 
   TYR   0.012   0.001   TYR R 625 
   ARG   0.011   0.000   ARG R 825 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 153
  average time/residue: 0.2649
  time to fit residues: 52.8447
Evaluate side-chains
  151 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0860
  time to fit residues: 1.7385
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.3980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8074  Z= 0.170
  Angle     :  0.573   9.141  10941  Z= 0.298
  Chirality :  0.042   0.139   1229
  Planarity :  0.004   0.082   1397
  Dihedral  :  4.447  17.849   1097
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.07 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.02 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.09 (0.28), residues: 989
  helix:  0.37 (0.30), residues: 327
  sheet: -0.47 (0.34), residues: 228
  loop : -1.69 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 234 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.032   0.001   PHE R 622 
   TYR   0.014   0.001   TYR R 625 
   ARG   0.011   0.000   ARG R 825 

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2796
  time to fit residues: 54.2310
Evaluate side-chains
  145 residues out of total 863 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.907 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1934
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0470
   chunk 79 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.111131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.090610 restraints weight = 14161.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.38
r_work: 0.3108 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8074  Z= 0.165
  Angle     :  0.580  11.666  10941  Z= 0.298
  Chirality :  0.042   0.226   1229
  Planarity :  0.004   0.081   1397
  Dihedral  :  4.369  17.048   1097
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.97 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 23.62 %
    Favored  : 76.26 %
  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: -0.95 (0.28), residues: 989
  helix:  0.48 (0.30), residues: 325
  sheet: -0.39 (0.34), residues: 227
  loop : -1.61 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 234 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.012   0.001   PHE R 622 
   TYR   0.014   0.001   TYR R 625 
   ARG   0.010   0.000   ARG R 825 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2210.44 seconds
wall clock time: 40 minutes 35.07 seconds (2435.07 seconds total)