Starting phenix.real_space_refine
on Tue Nov 14 21:17:26 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/11_2023/8jwg_36682_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/11_2023/8jwg_36682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/11_2023/8jwg_36682.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/11_2023/8jwg_36682.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/11_2023/8jwg_36682_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/11_2023/8jwg_36682_neut_updated.pdb"
  }
  resolution = 3.54
  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=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    6241      2.51       5
     N    1583      2.21       5
     O    1750      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    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: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 9620
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1192, 9594
          Classifications: {'peptide': 1192}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 26, 'TRANS': 1165}
          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
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'YMZ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.39, per 1000 atoms: 0.56
  Number of scatterers: 9620
  At special positions: 0
  Unit cell: (71.5, 111.1, 143, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     F       6      9.00
     O    1750      8.00
     N    1583      7.00
     C    6241      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: 3.72
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2262

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      55 helices and 3 sheets defined
      57.4% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 38
      removed outlier: 4.401A  pdb=" N   ASN A  37 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   GLU A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.667A  pdb=" N   LYS A  55 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU A  56 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LEU A  57 " --> pdb=" O   ARG A  54 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE A  59 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS A  63 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 71 through 85
      removed outlier: 3.726A  pdb=" N   SER A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   GLY A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 137
      removed outlier: 3.609A  pdb=" N   LEU A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ILE A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR A 114 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
    Processing helix  chain 'A' and resid 148 through 162
      removed outlier: 4.426A  pdb=" N   LEU A 155 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   ASP A 156 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 190
      removed outlier: 4.956A  pdb=" N   ILE A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   PHE A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
    Processing helix  chain 'A' and resid 203 through 239
      removed outlier: 3.662A  pdb=" N   LYS A 215 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ASN A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   THR A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 247
    Processing helix  chain 'A' and resid 251 through 304
      removed outlier: 4.320A  pdb=" N   LYS A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   PHE A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS A 278 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASN A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLY A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ILE A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   LEU A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 320 through 329
      removed outlier: 3.770A  pdb=" N   LEU A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 334
      No H-bonds generated for 'chain 'A' and resid 332 through 334'
    Processing helix  chain 'A' and resid 337 through 357
      removed outlier: 3.773A  pdb=" N   GLU A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   ILE A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 472 through 476
      removed outlier: 4.363A  pdb=" N   LYS A 476 " --> pdb=" O   ASN A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 488
      removed outlier: 4.926A  pdb=" N   ASP A 484 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   MET A 488 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 524
      removed outlier: 4.013A  pdb=" N   TYR A 524 " --> pdb=" O   MET A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 538
      removed outlier: 3.969A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 545
      No H-bonds generated for 'chain 'A' and resid 542 through 545'
    Processing helix  chain 'A' and resid 565 through 578
    Processing helix  chain 'A' and resid 596 through 606
    Processing helix  chain 'A' and resid 623 through 625
      No H-bonds generated for 'chain 'A' and resid 623 through 625'
    Processing helix  chain 'A' and resid 677 through 680
      No H-bonds generated for 'chain 'A' and resid 677 through 680'
    Processing helix  chain 'A' and resid 686 through 693
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 4.063A  pdb=" N   ILE A 778 " --> pdb=" O   ASN A 774 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER A 784 " --> pdb=" O   LYS A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 802
      removed outlier: 3.515A  pdb=" N   THR A 790 " --> pdb=" O   LYS A 786 " (cutoff:3.500A)
      removed outlier: 4.490A  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: 4.379A  pdb=" N   ALA A 811 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ARG A 812 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A 815 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 848
      removed outlier: 4.185A  pdb=" N   ILE A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   TYR A 833 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE A 834 " --> pdb=" O   TYR A 830 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE A 843 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 873
      removed outlier: 4.286A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL A 859 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLU A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ARG A 865 " --> pdb=" O   LYS A 861 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG A 866 " --> pdb=" O   THR A 862 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LEU A 872 " --> pdb=" O   PHE A 868 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   TYR A 873 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 880
    Processing helix  chain 'A' and resid 886 through 907
      removed outlier: 3.808A  pdb=" N   ILE A 893 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN A 894 " --> pdb=" O   SER A 890 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   VAL A 897 " --> pdb=" O   ILE A 893 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 904 " --> pdb=" O   LEU A 900 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 905 " --> pdb=" O   LYS A 901 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASN A 906 " --> pdb=" O   THR A 902 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASN A 907 " --> pdb=" O   GLY A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 926
      removed outlier: 3.674A  pdb=" N   MET A 922 " --> pdb=" O   PHE A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 944
      removed outlier: 3.951A  pdb=" N   VAL A 935 " --> pdb=" O   ILE A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 961
      removed outlier: 3.981A  pdb=" N   GLU A 960 " --> pdb=" O   SER A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 991
      removed outlier: 3.937A  pdb=" N   PHE A 990 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   TYR A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1034
      removed outlier: 4.512A  pdb=" N   TYR A1015 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASN A1017 " --> pdb=" O   ILE A1013 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LYS A1018 " --> pdb=" O   ASP A1014 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLY A1019 " --> pdb=" O   TYR A1015 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ARG A1022 " --> pdb=" O   LYS A1018 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TRP A1031 " --> pdb=" O   ASN A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1054
      removed outlier: 3.874A  pdb=" N   LEU A1052 " --> pdb=" O   PHE A1048 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A1053 " --> pdb=" O   GLY A1049 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LYS A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1080
      removed outlier: 3.636A  pdb=" N   THR A1069 " --> pdb=" O   LYS A1065 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   PHE A1070 " --> pdb=" O   SER A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1088 through 1097
      removed outlier: 3.859A  pdb=" N   GLU A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1101
      No H-bonds generated for 'chain 'A' and resid 1099 through 1101'
    Processing helix  chain 'A' and resid 1170 through 1174
    Processing helix  chain 'A' and resid 1244 through 1247
      No H-bonds generated for 'chain 'A' and resid 1244 through 1247'
    Processing helix  chain 'A' and resid 1265 through 1270
    Processing helix  chain 'A' and resid 1278 through 1287
      removed outlier: 3.698A  pdb=" N   LYS A1286 " --> pdb=" O   LYS A1282 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE A1287 " --> pdb=" O   ARG A1283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1296
      No H-bonds generated for 'chain 'A' and resid 1294 through 1296'
    Processing helix  chain 'A' and resid 1307 through 1309
      No H-bonds generated for 'chain 'A' and resid 1307 through 1309'
    Processing helix  chain 'A' and resid 1314 through 1327
    Processing helix  chain 'A' and resid 1344 through 1359
    Processing helix  chain 'A' and resid 1372 through 1377
      removed outlier: 5.247A  pdb=" N   ARG A1377 " --> pdb=" O   ALA A1373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1416
    Processing sheet with id=  A, first strand: chain 'A' and resid 1157 through 1161
      removed outlier: 6.560A  pdb=" N   LYS A1380 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   VAL A1160 " --> pdb=" O   LYS A1380 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   VAL A1382 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  A
    Processing sheet with id=  B, first strand: chain 'A' and resid 1251 through 1253
      removed outlier: 6.988A  pdb=" N   ILE A1332 " --> pdb=" O   SER A1252 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   THR A1364 " --> pdb=" O   LEU A1333 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'A' and resid 1126 through 1131
      removed outlier: 6.679A  pdb=" N   GLU A1231 " --> pdb=" O   LYS A1129 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1065 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: 2.83

  Time building geometry restraints manager: 4.04 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: 2971
        1.34 -     1.46: 1725
        1.46 -     1.58: 5037
        1.58 -     1.69: 0
        1.69 -     1.81: 67
  Bond restraints: 9800
  Sorted by residual:
  bond pdb=" CAR YMZ A1500 "
       pdb=" NAP YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.298  1.374 -0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" CAJ YMZ A1500 "
       pdb=" CAU YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.414  1.372  0.042 2.00e-02 2.50e+03 4.52e+00
  bond pdb=" CAS YMZ A1500 "
       pdb=" CAW YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.518  1.560 -0.042 2.00e-02 2.50e+03 4.50e+00
  bond pdb=" CAN YMZ A1500 "
       pdb=" NAQ YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.457  1.415  0.042 2.00e-02 2.50e+03 4.31e+00
  bond pdb=" CAZ YMZ A1500 "
       pdb=" FAE YMZ A1500 "
    ideal  model  delta    sigma   weight residual
    1.340  1.378 -0.038 2.00e-02 2.50e+03 3.56e+00
  ... (remaining 9795 not shown)

  Histogram of bond angle deviations from ideal:
       99.49 -   106.38: 156
      106.38 -   113.27: 5319
      113.27 -   120.17: 3653
      120.17 -   127.06: 4029
      127.06 -   133.95: 55
  Bond angle restraints: 13212
  Sorted by residual:
  angle pdb=" C   ASN A 440 "
        pdb=" N   ASP A 441 "
        pdb=" CA  ASP A 441 "
      ideal   model   delta    sigma   weight residual
     122.08  128.80   -6.72 1.47e+00 4.63e-01 2.09e+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  127.62   -6.08 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" N   LEU A1001 "
        pdb=" CA  LEU A1001 "
        pdb=" C   LEU A1001 "
      ideal   model   delta    sigma   weight residual
     112.72  108.74    3.98 1.28e+00 6.10e-01 9.67e+00
  angle pdb=" CA  ASN A1106 "
        pdb=" CB  ASN A1106 "
        pdb=" CG  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     112.60  115.57   -2.97 1.00e+00 1.00e+00 8.79e+00
  angle pdb=" C   SER A1105 "
        pdb=" N   ASN A1106 "
        pdb=" CA  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     122.61  127.03   -4.42 1.56e+00 4.11e-01 8.04e+00
  ... (remaining 13207 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 5712
       17.92 -    35.84: 175
       35.84 -    53.76: 14
       53.76 -    71.68: 2
       71.68 -    89.60: 3
  Dihedral angle restraints: 5906
    sinusoidal: 2401
      harmonic: 3505
  Sorted by residual:
  dihedral pdb=" CA  TYR A1004 "
           pdb=" C   TYR A1004 "
           pdb=" N   PHE A1005 "
           pdb=" CA  PHE A1005 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ARG A 776 "
           pdb=" C   ARG A 776 "
           pdb=" N   ILE A 777 "
           pdb=" CA  ILE A 777 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  ARG A 428 "
           pdb=" C   ARG A 428 "
           pdb=" N   LEU A 429 "
           pdb=" CA  LEU A 429 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.62   20.38     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5903 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 994
       0.037 -    0.074: 376
       0.074 -    0.111: 105
       0.111 -    0.148: 33
       0.148 -    0.185: 6
  Chirality restraints: 1514
  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    2.83   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  ASN A 440 "
            pdb=" N   ASN A 440 "
            pdb=" C   ASN A 440 "
            pdb=" CB  ASN A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.83e-01
  chirality pdb=" CAX YMZ A1500 "
            pdb=" CAO YMZ A1500 "
            pdb=" CAW YMZ A1500 "
            pdb=" NAQ YMZ A1500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -2.56    0.17 2.00e-01 2.50e+01 6.83e-01
  ... (remaining 1511 not shown)

  Planarity restraints: 1638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 290 "   -0.019 2.00e-02 2.50e+03   1.38e-02 3.82e+00
        pdb=" CG  TYR A 290 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 290 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 290 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 290 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 290 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 290 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 290 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1257 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A1258 "    0.084 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=" C   LEU A  71 "   -0.031 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO A  72 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1635 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1470
        2.76 -     3.29: 10031
        3.29 -     3.83: 14280
        3.83 -     4.36: 17360
        4.36 -     4.90: 29029
  Nonbonded interactions: 72170
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 822 "
            pdb=" ND2 ASN A 826 "
     model   vdw
     2.223 2.520
  nonbonded pdb=" OD2 ASP A 144 "
            pdb=" OH  TYR A 430 "
     model   vdw
     2.232 2.440
  nonbonded pdb=" O   PRO A 338 "
            pdb=" OG1 THR A 341 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" O   LYS A 220 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" NE  ARG A1116 "
            pdb=" OD2 ASP A1246 "
     model   vdw
     2.267 2.520
  ... (remaining 72165 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:          4.010
  Check model and map are aligned:         0.150
  Set scattering table:                    0.080
  Process input model:                     28.090
  Find NCS groups from input model:        0.240
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
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   0.076   9800  Z= 0.297
  Angle     :  0.721   6.724  13212  Z= 0.399
  Chirality :  0.044   0.185   1514
  Planarity :  0.004   0.049   1638
  Dihedral  :  9.343  89.598   3644
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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: -3.71 (0.20), residues: 1178
  helix: -1.90 (0.16), residues: 658
  sheet: -3.26 (0.73), residues: 34
  loop : -3.12 (0.25), residues: 486

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.2756
  time to fit residues: 90.4481
Evaluate side-chains
  108 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.105 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6162
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   chunk 60 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 93 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:    9.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 994 HIS
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1243 ASN
A1370 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.105   9800  Z= 0.470
  Angle     :  0.833  10.075  13212  Z= 0.444
  Chirality :  0.053   0.239   1514
  Planarity :  0.005   0.055   1638
  Dihedral  :  5.914  53.072   1295
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  9.68 %
    Favored  : 87.90 %
  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: -3.35 (0.20), residues: 1178
  helix: -1.52 (0.17), residues: 688
  sheet: -3.32 (0.66), residues: 36
  loop : -3.14 (0.24), residues: 454

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 21
  residues processed: 128
  average time/residue: 0.2243
  time to fit residues: 40.1841
Evaluate side-chains
  112 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 1.105 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1101
  time to fit residues: 5.4851
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 108 optimal weight:    4.9990
   chunk 116 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 853 ASN
A 894 ASN
A 998 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9800  Z= 0.174
  Angle     :  0.603  11.081  13212  Z= 0.312
  Chirality :  0.043   0.149   1514
  Planarity :  0.004   0.045   1638
  Dihedral  :  5.256  49.342   1295
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 12.38 %
    Favored  : 87.15 %
  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: -2.21 (0.22), residues: 1178
  helix: -0.52 (0.19), residues: 672
  sheet: -2.48 (0.66), residues: 45
  loop : -2.76 (0.25), residues: 461

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 118
  average time/residue: 0.2387
  time to fit residues: 40.0051
Evaluate side-chains
  101 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 1.240 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1128
  time to fit residues: 2.2358
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.4980
   chunk 81 optimal weight:    0.5980
   chunk 56 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0970
   chunk 72 optimal weight:    8.9990
   chunk 108 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0010
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.8386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9800  Z= 0.159
  Angle     :  0.571  11.456  13212  Z= 0.292
  Chirality :  0.042   0.147   1514
  Planarity :  0.003   0.049   1638
  Dihedral  :  4.893  44.767   1295
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.87 %
    Favored  : 84.45 %
  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: -1.69 (0.23), residues: 1178
  helix: -0.14 (0.19), residues: 682
  sheet: -1.55 (0.83), residues: 35
  loop : -2.60 (0.25), residues: 461

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 8
  residues processed: 123
  average time/residue: 0.2368
  time to fit residues: 41.1338
Evaluate side-chains
  106 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 1.100 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0959
  time to fit residues: 2.8934
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0770
   chunk 85 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 98 optimal weight:    0.2980
   chunk 79 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 58 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.8338

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

Flipped N/Q/H residues before XYZ refinement:
A 542 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.4433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9800  Z= 0.154
  Angle     :  0.574  14.709  13212  Z= 0.289
  Chirality :  0.041   0.142   1514
  Planarity :  0.003   0.045   1638
  Dihedral  :  4.687  39.510   1295
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.18 %
    Favored  : 83.24 %
  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: -1.36 (0.24), residues: 1178
  helix:  0.10 (0.20), residues: 689
  sheet: -1.14 (0.87), residues: 35
  loop : -2.48 (0.26), residues: 454

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2210
  time to fit residues: 37.3454
Evaluate side-chains
  111 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 1.094 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0966
  time to fit residues: 3.0346
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    0.0980
   chunk 22 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 115 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 111 optimal weight:    8.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9800  Z= 0.240
  Angle     :  0.631  11.241  13212  Z= 0.325
  Chirality :  0.044   0.149   1514
  Planarity :  0.003   0.040   1638
  Dihedral  :  4.877  28.840   1295
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.36 %
    Favored  : 83.15 %
  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: -1.48 (0.23), residues: 1178
  helix:  0.02 (0.19), residues: 681
  sheet: -1.44 (0.83), residues: 40
  loop : -2.49 (0.26), residues: 457

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 13
  residues processed: 116
  average time/residue: 0.2144
  time to fit residues: 36.0671
Evaluate side-chains
  116 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 1.015 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0961
  time to fit residues: 3.6670
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0670
   chunk 114 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9800  Z= 0.148
  Angle     :  0.562  11.665  13212  Z= 0.287
  Chirality :  0.041   0.140   1514
  Planarity :  0.003   0.039   1638
  Dihedral  :  4.589  24.711   1295
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 16.29 %
    Favored  : 83.24 %
  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 (0.24), residues: 1178
  helix:  0.30 (0.20), residues: 679
  sheet: -1.14 (0.83), residues: 40
  loop : -2.37 (0.26), residues: 459

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 113
  average time/residue: 0.2397
  time to fit residues: 38.1568
Evaluate side-chains
  105 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 1.209 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0894
  time to fit residues: 2.1953
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0370
   chunk 10 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0970
   overall best weight:    0.6256

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9800  Z= 0.143
  Angle     :  0.550  10.912  13212  Z= 0.280
  Chirality :  0.040   0.141   1514
  Planarity :  0.003   0.039   1638
  Dihedral  :  4.370  20.620   1295
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 17.23 %
    Favored  : 82.50 %
  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: -0.96 (0.24), residues: 1178
  helix:  0.47 (0.20), residues: 681
  sheet: -1.03 (0.82), residues: 40
  loop : -2.35 (0.26), residues: 457

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 111
  average time/residue: 0.2064
  time to fit residues: 33.4121
Evaluate side-chains
  103 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 1.041 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1242
  time to fit residues: 1.5999
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0670
   chunk 96 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.9322

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 998 ASN
** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.5390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9800  Z= 0.241
  Angle     :  0.646  12.596  13212  Z= 0.331
  Chirality :  0.044   0.151   1514
  Planarity :  0.003   0.041   1638
  Dihedral  :  4.700  19.140   1295
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.67 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.23), residues: 1178
  helix:  0.19 (0.20), residues: 683
  sheet: -1.01 (0.84), residues: 40
  loop : -2.45 (0.25), residues: 455

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2517
  time to fit residues: 38.5505
Evaluate side-chains
  106 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.084 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0975
  time to fit residues: 3.3574
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 72 optimal weight:    0.2980
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 ASN
** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9800  Z= 0.149
  Angle     :  0.579  12.630  13212  Z= 0.293
  Chirality :  0.041   0.140   1514
  Planarity :  0.003   0.039   1638
  Dihedral  :  4.374  18.645   1295
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 17.04 %
    Favored  : 82.87 %
  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: -0.96 (0.24), residues: 1178
  helix:  0.42 (0.20), residues: 687
  sheet: -0.85 (0.84), residues: 40
  loop : -2.32 (0.26), residues: 451

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 0.2049
  time to fit residues: 31.1851
Evaluate side-chains
  100 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 1.149 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1252
  time to fit residues: 1.8107
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.0980
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 94 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1268 ASN ** 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 = 0.4568 r_free = 0.4568 target = 0.160874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.122037 restraints weight = 18025.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.125159 restraints weight = 8198.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.128703 restraints weight = 4126.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.5538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9800  Z= 0.182
  Angle     :  0.593  12.253  13212  Z= 0.301
  Chirality :  0.042   0.154   1514
  Planarity :  0.003   0.040   1638
  Dihedral  :  4.407  18.994   1295
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 17.50 %
    Favored  : 82.40 %
  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: -0.96 (0.24), residues: 1178
  helix:  0.42 (0.20), residues: 692
  sheet: -0.83 (0.84), residues: 40
  loop : -2.34 (0.26), residues: 446
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1980.65 seconds
wall clock time: 37 minutes 5.89 seconds (2225.89 seconds total)