Starting phenix.real_space_refine
on Tue Nov 14 21:57:09 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/11_2023/8jvh_36674_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/11_2023/8jvh_36674.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/11_2023/8jvh_36674.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/11_2023/8jvh_36674.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/11_2023/8jvh_36674_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/11_2023/8jvh_36674_neut.pdb"
  }
  resolution = 3.19
  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=  -0.003 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    6289      2.51       5
     N    1599      2.21       5
     O    1771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  401": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  575": "NH1" <-> "NH2"
    Residue "A ARG  614": "NH1" <-> "NH2"
    Residue "A ARG  627": "NH1" <-> "NH2"
    Residue "A ARG 1138": "NH1" <-> "NH2"
    Residue "A ARG 1176": "NH1" <-> "NH2"
    Residue "A ARG 1371": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 9699
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1205, 9699
          Classifications: {'peptide': 1205}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 26, 'TRANS': 1178}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.07, per 1000 atoms: 0.52
  Number of scatterers: 9699
  At special positions: 0
  Unit cell: (72.6, 119.9, 144.1, 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      40     16.00
     O    1771      8.00
     N    1599      7.00
     C    6289      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: 3.78
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 7 sheets defined
      62.7% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 24
      removed outlier: 3.645A  pdb=" N   GLU A  22 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 37
      removed outlier: 3.694A  pdb=" N   ARG A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN A  37 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 48
      removed outlier: 3.622A  pdb=" N   LYS A  47 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   CYS A  48 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 44 through 48'
    Processing helix  chain 'A' and resid 55 through 66
      removed outlier: 3.668A  pdb=" N   ALA A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 69
      No H-bonds generated for 'chain 'A' and resid 67 through 69'
    Processing helix  chain 'A' and resid 70 through 86
      removed outlier: 3.823A  pdb=" N   SER A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   GLY A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 137
      removed outlier: 4.102A  pdb=" N   SER A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ILE A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLY A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   TYR A 114 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ILE A 119 " --> pdb=" O   CYS A 115 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LYS A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ARG A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 146
      removed outlier: 3.915A  pdb=" N   ASN A 145 " --> pdb=" O   GLN A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 149
      No H-bonds generated for 'chain 'A' and resid 147 through 149'
    Processing helix  chain 'A' and resid 150 through 159
      removed outlier: 4.017A  pdb=" N   ASP A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   PHE A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 170
      removed outlier: 3.894A  pdb=" N   PHE A 170 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 167 through 170'
    Processing helix  chain 'A' and resid 171 through 191
      removed outlier: 3.790A  pdb=" N   THR A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   TYR A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASN A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 3.887A  pdb=" N   THR A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   CYS A 197 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 240
      removed outlier: 3.975A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS A 215 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR A 226 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASN A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ASN A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   THR A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
      removed outlier: 3.858A  pdb=" N   SER A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 303
      removed outlier: 3.682A  pdb=" N   THR A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   PHE A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   TYR A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   HIS A 278 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ILE A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ILE A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   LEU A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG A 299 " --> pdb=" O   TRP A 295 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE A 302 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASN A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 318
      removed outlier: 3.681A  pdb=" N   SER A 318 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 315 through 318'
    Processing helix  chain 'A' and resid 319 through 334
      removed outlier: 3.797A  pdb=" N   LEU A 323 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   MET A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   MET A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LEU A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 351
      removed outlier: 3.565A  pdb=" N   ILE A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 444 through 448
      removed outlier: 3.552A  pdb=" N   ILE A 448 " --> pdb=" O   LEU A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 454
    Processing helix  chain 'A' and resid 471 through 477
      removed outlier: 3.842A  pdb=" N   ILE A 475 " --> pdb=" O   ILE A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 488
      removed outlier: 3.894A  pdb=" N   LEU A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU A 486 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA A 487 " --> pdb=" O   LYS A 483 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   MET A 488 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 529 through 539
      removed outlier: 3.697A  pdb=" N   VAL A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL A 539 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 548
      removed outlier: 3.775A  pdb=" N   LEU A 548 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 579
      removed outlier: 4.558A  pdb=" N   ARG A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 607
      removed outlier: 3.688A  pdb=" N   GLU A 598 " --> pdb=" O   ASP A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 694
      removed outlier: 3.547A  pdb=" N   LEU A 689 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 783
      removed outlier: 3.837A  pdb=" N   ILE A 778 " --> pdb=" O   ASN A 774 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE A 783 " --> pdb=" O   TYR A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 803
      removed outlier: 3.761A  pdb=" N   VAL A 789 " --> pdb=" O   TYR A 785 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   THR A 790 " --> pdb=" O   LYS A 786 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ILE A 791 " --> pdb=" O   LYS A 787 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE A 792 " --> pdb=" O   ASP A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 815
      removed outlier: 3.837A  pdb=" N   LEU A 808 " --> pdb=" O   PRO A 804 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL A 814 " --> pdb=" O   TYR A 810 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A 815 " --> pdb=" O   ALA A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 873
      removed outlier: 3.746A  pdb=" N   ASN A 826 " --> pdb=" O   ASN A 822 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR A 833 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ILE A 834 " --> pdb=" O   TYR A 830 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE A 843 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   TYR A 851 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASN A 852 " --> pdb=" O   LYS A 848 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASN A 853 " --> pdb=" O   ASN A 849 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL A 859 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ARG A 865 " --> pdb=" O   LYS A 861 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ARG A 866 " --> pdb=" O   THR A 862 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 872 " --> pdb=" O   PHE A 868 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   TYR A 873 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 881
      removed outlier: 4.115A  pdb=" N   PHE A 879 " --> pdb=" O   GLU A 875 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN A 881 " --> pdb=" O   SER A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 903
      removed outlier: 4.001A  pdb=" N   ILE A 893 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ASN A 894 " --> pdb=" O   SER A 890 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   VAL A 897 " --> pdb=" O   ILE A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 927
      removed outlier: 5.210A  pdb=" N   VAL A 909 " --> pdb=" O   VAL A 905 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL A 920 " --> pdb=" O   MET A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 945
      removed outlier: 3.768A  pdb=" N   ALA A 933 " --> pdb=" O   CYS A 929 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA A 934 " --> pdb=" O   PRO A 930 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   VAL A 935 " --> pdb=" O   ILE A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 963
      removed outlier: 4.068A  pdb=" N   ILE A 959 " --> pdb=" O   LYS A 955 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLU A 960 " --> pdb=" O   SER A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 991
      removed outlier: 3.715A  pdb=" N   PHE A 990 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 986 through 991'
    Processing helix  chain 'A' and resid 992 through 997
      removed outlier: 3.783A  pdb=" N   VAL A 996 " --> pdb=" O   ASN A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1014
    Processing helix  chain 'A' and resid 1016 through 1036
      removed outlier: 4.364A  pdb=" N   ARG A1022 " --> pdb=" O   LYS A1018 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A1029 " --> pdb=" O   ILE A1025 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TRP A1031 " --> pdb=" O   ASN A1027 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A1033 " --> pdb=" O   ALA A1029 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1054
      removed outlier: 4.006A  pdb=" N   LYS A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1081
      removed outlier: 3.799A  pdb=" N   PHE A1068 " --> pdb=" O   MET A1064 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   THR A1069 " --> pdb=" O   LYS A1065 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   PHE A1070 " --> pdb=" O   SER A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1097
      removed outlier: 3.998A  pdb=" N   ALA A1090 " --> pdb=" O   ASP A1086 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS A1091 " --> pdb=" O   SER A1087 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A1094 " --> pdb=" O   ALA A1090 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLU A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1175
    Processing helix  chain 'A' and resid 1240 through 1242
      No H-bonds generated for 'chain 'A' and resid 1240 through 1242'
    Processing helix  chain 'A' and resid 1264 through 1270
      removed outlier: 3.532A  pdb=" N   LYS A1270 " --> pdb=" O   TYR A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1288
      removed outlier: 3.846A  pdb=" N   VAL A1281 " --> pdb=" O   THR A1277 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE A1287 " --> pdb=" O   ARG A1283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1293 through 1297
      removed outlier: 3.928A  pdb=" N   LEU A1297 " --> pdb=" O   ILE A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1303
      removed outlier: 4.001A  pdb=" N   THR A1303 " --> pdb=" O   LYS A1300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1310
    Processing helix  chain 'A' and resid 1313 through 1327
      removed outlier: 3.823A  pdb=" N   GLN A1318 " --> pdb=" O   GLY A1314 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ARG A1319 " --> pdb=" O   GLY A1315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1343 through 1358
    Processing helix  chain 'A' and resid 1371 through 1378
      removed outlier: 4.403A  pdb=" N   ARG A1377 " --> pdb=" O   ALA A1373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379
    Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411
      removed outlier: 4.016A  pdb=" N   ILE A 618 " --> pdb=" O   TYR A 409 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460
      removed outlier: 6.082A  pdb=" N   GLY A 458 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 636
      removed outlier: 4.613A  pdb=" N   SER A 636 " --> pdb=" O   TYR A 669 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR A 669 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1149 through 1151
      removed outlier: 6.319A  pdb=" N   GLU A1231 " --> pdb=" O   LYS A1129 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1161
      removed outlier: 6.618A  pdb=" N   ALA A1158 " --> pdb=" O   VAL A1382 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   PHE A1384 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A1160 " --> pdb=" O   PHE A1384 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN A1385 " --> pdb=" O   PHE A1393 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE A1393 " --> pdb=" O   ASN A1385 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1251 through 1254

    421 hydrogen bonds defined for protein.
    1227 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: 3.06

  Time building geometry restraints manager: 4.14 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: 3013
        1.34 -     1.46: 1987
        1.46 -     1.58: 4809
        1.58 -     1.70: 0
        1.70 -     1.82: 67
  Bond restraints: 9876
  Sorted by residual:
  bond pdb=" CB  ASP A 441 "
       pdb=" CG  ASP A 441 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 2.50e-02 1.60e+03 2.00e+00
  bond pdb=" CG  LEU A1080 "
       pdb=" CD2 LEU A1080 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.97e+00
  bond pdb=" CA  LEU A 362 "
       pdb=" C   LEU A 362 "
    ideal  model  delta    sigma   weight residual
    1.523  1.543 -0.021 1.49e-02 4.50e+03 1.92e+00
  bond pdb=" C   ILE A 328 "
       pdb=" N   SER A 329 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.31e-02 5.83e+03 1.89e+00
  bond pdb=" CB  ASN A1106 "
       pdb=" CG  ASN A1106 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.74e+00
  ... (remaining 9871 not shown)

  Histogram of bond angle deviations from ideal:
       99.24 -   106.21: 142
      106.21 -   113.17: 5305
      113.17 -   120.14: 3840
      120.14 -   127.11: 3960
      127.11 -   134.08: 58
  Bond angle restraints: 13305
  Sorted by residual:
  angle pdb=" C   SER A1105 "
        pdb=" N   ASN A1106 "
        pdb=" CA  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     121.54  131.63  -10.09 1.91e+00 2.74e-01 2.79e+01
  angle pdb=" C   ASN A 440 "
        pdb=" N   ASP A 441 "
        pdb=" CA  ASP A 441 "
      ideal   model   delta    sigma   weight residual
     121.54  128.60   -7.06 1.91e+00 2.74e-01 1.37e+01
  angle pdb=" C   ALA A 821 "
        pdb=" N   ASN A 822 "
        pdb=" CA  ASN A 822 "
      ideal   model   delta    sigma   weight residual
     121.54  127.58   -6.04 1.91e+00 2.74e-01 9.99e+00
  angle pdb=" CA  ASN A1106 "
        pdb=" CB  ASN A1106 "
        pdb=" CG  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     112.60  115.68   -3.08 1.00e+00 1.00e+00 9.50e+00
  angle pdb=" C   PRO A 361 "
        pdb=" N   LEU A 362 "
        pdb=" CA  LEU A 362 "
      ideal   model   delta    sigma   weight residual
     123.91  128.78   -4.87 1.66e+00 3.63e-01 8.62e+00
  ... (remaining 13300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 5645
       15.07 -    30.15: 274
       30.15 -    45.22: 51
       45.22 -    60.30: 1
       60.30 -    75.37: 3
  Dihedral angle restraints: 5974
    sinusoidal: 2431
      harmonic: 3543
  Sorted by residual:
  dihedral pdb=" CA  VAL A 905 "
           pdb=" C   VAL A 905 "
           pdb=" N   ASN A 906 "
           pdb=" CA  ASN A 906 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.25   25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  CYS A1151 "
           pdb=" C   CYS A1151 "
           pdb=" N   ASP A1152 "
           pdb=" CA  ASP A1152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.65  -24.35     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  LYS A1016 "
           pdb=" C   LYS A1016 "
           pdb=" N   ASN A1017 "
           pdb=" CA  ASN A1017 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.32  -23.68     0      5.00e+00 4.00e-02 2.24e+01
  ... (remaining 5971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 987
       0.039 -    0.079: 401
       0.079 -    0.118: 116
       0.118 -    0.157: 22
       0.157 -    0.196: 3
  Chirality restraints: 1529
  Sorted by residual:
  chirality pdb=" CB  ILE A 437 "
            pdb=" CA  ILE A 437 "
            pdb=" CG1 ILE A 437 "
            pdb=" CG2 ILE A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.20 2.00e-01 2.50e+01 9.63e-01
  chirality pdb=" CA  ASN A1106 "
            pdb=" N   ASN A1106 "
            pdb=" C   ASN A1106 "
            pdb=" CB  ASN A1106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" CA  ASP A 441 "
            pdb=" N   ASP A 441 "
            pdb=" C   ASP A 441 "
            pdb=" CB  ASP A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 1526 not shown)

  Planarity restraints: 1654
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 437 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.29e+00
        pdb=" C   ILE A 437 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A 437 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 438 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1257 "    0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A1258 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A1258 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1258 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 440 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   ASN A 440 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASN A 440 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASP A 441 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1651 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 610
        2.74 -     3.28: 10110
        3.28 -     3.82: 13912
        3.82 -     4.36: 17111
        4.36 -     4.90: 29368
  Nonbonded interactions: 71111
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 286 "
            pdb=" OG  SER A 289 "
     model   vdw
     2.195 2.440
  nonbonded pdb=" O   ILE A1375 "
            pdb=" OG  SER A1378 "
     model   vdw
     2.244 2.440
  nonbonded pdb=" OD2 ASP A 144 "
            pdb=" OH  TYR A 430 "
     model   vdw
     2.253 2.440
  nonbonded pdb=" O   PRO A 338 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.255 2.440
  nonbonded pdb=" ND2 ASN A 774 "
            pdb=" OE1 GLU A1095 "
     model   vdw
     2.264 2.520
  ... (remaining 71106 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:             1.040
  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:          4.620
  Check model and map are aligned:         0.150
  Set scattering table:                    0.110
  Process input model:                     28.230
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
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   0.052   9876  Z= 0.337
  Angle     :  0.785  10.087  13305  Z= 0.442
  Chirality :  0.046   0.196   1529
  Planarity :  0.004   0.050   1654
  Dihedral  :  9.557  75.370   3686
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.21 %
    Favored  : 97.61 %
  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: -4.48 (0.19), residues: 1191
  helix: -2.45 (0.16), residues: 713
  sheet: -3.43 (0.53), residues: 56
  loop : -3.61 (0.24), residues: 422

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2773
  time to fit residues: 71.4972
Evaluate side-chains
  95 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.150 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5332
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 108 optimal weight:    0.0870
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
A 283 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 894 ASN
A 992 ASN
A1256 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9876  Z= 0.218
  Angle     :  0.628  10.276  13305  Z= 0.327
  Chirality :  0.044   0.177   1529
  Planarity :  0.004   0.043   1654
  Dihedral  :  5.202  24.029   1301
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  7.91 %
    Favored  : 90.71 %
  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: -3.09 (0.22), residues: 1191
  helix: -1.33 (0.18), residues: 721
  sheet: -2.94 (0.57), residues: 61
  loop : -3.06 (0.26), residues: 409

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2343
  time to fit residues: 42.4328
Evaluate side-chains
  96 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.061 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0956
  time to fit residues: 3.4457
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0050
   chunk 109 optimal weight:    7.9990
   chunk 117 optimal weight:   10.0000
   chunk 97 optimal weight:    0.4980
   chunk 108 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 87 optimal weight:    0.0970
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9876  Z= 0.137
  Angle     :  0.524   9.364  13305  Z= 0.275
  Chirality :  0.041   0.156   1529
  Planarity :  0.003   0.041   1654
  Dihedral  :  4.659  21.599   1301
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  9.57 %
    Favored  : 89.42 %
  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: -2.28 (0.23), residues: 1191
  helix: -0.66 (0.19), residues: 725
  sheet: -2.49 (0.62), residues: 62
  loop : -2.82 (0.25), residues: 404

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 101
  average time/residue: 0.2349
  time to fit residues: 33.9913
Evaluate side-chains
  88 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 1.193 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1101
  time to fit residues: 2.3936
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 73 optimal weight:    0.2980
   chunk 109 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9876  Z= 0.190
  Angle     :  0.552   8.611  13305  Z= 0.292
  Chirality :  0.043   0.164   1529
  Planarity :  0.003   0.043   1654
  Dihedral  :  4.569  21.430   1301
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.40 %
    Favored  : 88.41 %
  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: -1.92 (0.23), residues: 1191
  helix: -0.39 (0.19), residues: 731
  sheet: -2.20 (0.65), residues: 64
  loop : -2.69 (0.26), residues: 396

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 5
  residues processed: 108
  average time/residue: 0.2476
  time to fit residues: 37.2364
Evaluate side-chains
  89 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 1.097 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0891
  time to fit residues: 2.4236
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    0.1980
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9876  Z= 0.158
  Angle     :  0.508   8.072  13305  Z= 0.269
  Chirality :  0.042   0.192   1529
  Planarity :  0.003   0.043   1654
  Dihedral  :  4.444  20.840   1301
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.96 %
    Favored  : 86.94 %
  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: -1.60 (0.24), residues: 1191
  helix: -0.15 (0.19), residues: 733
  sheet: -2.31 (0.62), residues: 74
  loop : -2.49 (0.28), residues: 384

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 3
  residues processed: 104
  average time/residue: 0.2691
  time to fit residues: 39.1682
Evaluate side-chains
  88 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 1.044 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1041
  time to fit residues: 2.0958
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 104 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0870
   chunk 116 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    1.4762

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9876  Z= 0.241
  Angle     :  0.574   8.195  13305  Z= 0.306
  Chirality :  0.044   0.199   1529
  Planarity :  0.004   0.045   1654
  Dihedral  :  4.597  21.270   1301
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.42 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.66 (0.24), residues: 1191
  helix: -0.18 (0.19), residues: 731
  sheet: -2.06 (0.65), residues: 64
  loop : -2.59 (0.27), residues: 396

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 7
  residues processed: 93
  average time/residue: 0.2590
  time to fit residues: 33.6170
Evaluate side-chains
  91 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 1.141 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0896
  time to fit residues: 2.6509
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    0.0040
   chunk 13 optimal weight:    8.9990
   chunk 66 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 64 optimal weight:    0.6980
   chunk 115 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9876  Z= 0.141
  Angle     :  0.514   8.226  13305  Z= 0.271
  Chirality :  0.041   0.225   1529
  Planarity :  0.003   0.045   1654
  Dihedral  :  4.358  20.338   1301
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 13.25 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.31 (0.24), residues: 1191
  helix:  0.12 (0.19), residues: 739
  sheet: -2.15 (0.61), residues: 73
  loop : -2.52 (0.28), residues: 379

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 86
  average time/residue: 0.2676
  time to fit residues: 31.8836
Evaluate side-chains
  85 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 1.161 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1066
  time to fit residues: 2.0044
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0980
   chunk 22 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 78 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 90 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0980
   overall best weight:    0.2580

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

Flipped N/Q/H residues before XYZ refinement:
A 365 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9876  Z= 0.110
  Angle     :  0.474  10.275  13305  Z= 0.249
  Chirality :  0.040   0.251   1529
  Planarity :  0.003   0.045   1654
  Dihedral  :  3.960  17.450   1301
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 13.62 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.73 (0.25), residues: 1191
  helix:  0.60 (0.20), residues: 731
  sheet: -2.06 (0.60), residues: 78
  loop : -2.24 (0.29), residues: 382

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2675
  time to fit residues: 37.5080
Evaluate side-chains
  87 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 1.088 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0865
  time to fit residues: 1.7293
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0470
   chunk 84 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 70 optimal weight:    0.4980
   chunk 113 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9876  Z= 0.130
  Angle     :  0.488  10.593  13305  Z= 0.256
  Chirality :  0.041   0.254   1529
  Planarity :  0.003   0.045   1654
  Dihedral  :  3.942  17.599   1301
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 14.26 %
    Favored  : 85.46 %
  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: -0.60 (0.25), residues: 1191
  helix:  0.74 (0.20), residues: 729
  sheet: -2.07 (0.63), residues: 73
  loop : -2.24 (0.28), residues: 389

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 96
  average time/residue: 0.2634
  time to fit residues: 34.9175
Evaluate side-chains
  92 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 1.124 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0902
  time to fit residues: 1.7997
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.0010
   chunk 79 optimal weight:    0.8980
   chunk 119 optimal weight:    8.9990
   chunk 110 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0470
   chunk 75 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.4684

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.4647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9876  Z= 0.123
  Angle     :  0.486  10.635  13305  Z= 0.255
  Chirality :  0.041   0.248   1529
  Planarity :  0.003   0.044   1654
  Dihedral  :  3.905  17.375   1301
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 14.63 %
    Favored  : 85.19 %
  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: -0.47 (0.25), residues: 1191
  helix:  0.79 (0.20), residues: 735
  sheet: -2.04 (0.62), residues: 73
  loop : -2.10 (0.29), residues: 383

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2734
  time to fit residues: 36.1057
Evaluate side-chains
  89 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.084 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5496
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.178848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.121405 restraints weight = 12985.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.91
r_work: 0.3440 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.4691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9876  Z= 0.147
  Angle     :  0.502  10.647  13305  Z= 0.264
  Chirality :  0.042   0.247   1529
  Planarity :  0.003   0.044   1654
  Dihedral  :  3.962  17.696   1301
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 14.72 %
    Favored  : 85.10 %
  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: -0.47 (0.25), residues: 1191
  helix:  0.80 (0.20), residues: 729
  sheet: -1.97 (0.63), residues: 73
  loop : -2.11 (0.29), residues: 389
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2232.14 seconds
wall clock time: 41 minutes 31.07 seconds (2491.07 seconds total)