Starting phenix.real_space_refine (version: dev)
on Fri May 13 02:28:22 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/05_2022/6lr0_31583.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/05_2022/6lr0_31583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/05_2022/6lr0_31583.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/05_2022/6lr0_31583.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/05_2022/6lr0_31583.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/05_2022/6lr0_31583.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.098
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "U ARG   44": "NH1" <-> "NH2"
    Residue "U PHE   51": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ARG  184": "NH1" <-> "NH2"
    Residue "U ARG  237": "NH1" <-> "NH2"
    Residue "U ARG  289": "NH1" <-> "NH2"
    Residue "U ARG  299": "NH1" <-> "NH2"
    Residue "U ARG  317": "NH1" <-> "NH2"
    Residue "U ARG  415": "NH1" <-> "NH2"
    Residue "U ARG  432": "NH1" <-> "NH2"
    Residue "U ARG  487": "NH1" <-> "NH2"
    Residue "U ARG  571": "NH1" <-> "NH2"
    Residue "U ARG  575": "NH1" <-> "NH2"
    Residue "U ARG  637": "NH1" <-> "NH2"
    Residue "U ARG  646": "NH1" <-> "NH2"
    Residue "U ARG  692": "NH1" <-> "NH2"
    Residue "U ARG  832": "NH1" <-> "NH2"
    Residue "U ARG  860": "NH1" <-> "NH2"
    Residue "U ARG  920": "NH1" <-> "NH2"
    Residue "U ARG  958": "NH1" <-> "NH2"
    Residue "U ARG 1019": "NH1" <-> "NH2"
    Residue "U ARG 1187": "NH1" <-> "NH2"
    Residue "U ARG 1221": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib"
  Total number of atoms: 9576
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "U"
      Number of atoms: 9576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1230, 9576
          Classifications: {'peptide': 1230}
          Link IDs: {'PTRANS': 36, 'TRANS': 1193}
          Chain breaks: 2
  Time building chain proxies: 5.99, per 1000 atoms: 0.63
  Number of scatterers: 9576
  At special positions: 0
  Unit cell: (90.1, 160.06, 112.36, 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      54     16.00
     O    1766      8.00
     N    1627      7.00
     C    6129      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: 3.82
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2272

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 4 sheets defined
      36.3% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'U' and resid 46 through 50
    Processing helix  chain 'U' and resid 79 through 84
    Processing helix  chain 'U' and resid 88 through 100
      removed outlier: 3.716A  pdb=" N   GLU U  96 " --> pdb=" O   ASP U  92 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU U  99 " --> pdb=" O   VAL U  95 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 147 through 155
      removed outlier: 4.004A  pdb=" N   LEU U 153 " --> pdb=" O   ALA U 149 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 173 through 183
      removed outlier: 3.655A  pdb=" N   PHE U 179 " --> pdb=" O   ARG U 175 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 187 through 192
      removed outlier: 3.734A  pdb=" N   PHE U 190 " --> pdb=" O   ILE U 187 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   CYS U 192 " --> pdb=" O   TRP U 189 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 230 through 238
      removed outlier: 3.769A  pdb=" N   PHE U 236 " --> pdb=" O   LEU U 232 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG U 237 " --> pdb=" O   LEU U 233 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY U 238 " --> pdb=" O   GLY U 234 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 240 through 245
      removed outlier: 3.740A  pdb=" N   VAL U 244 " --> pdb=" O   LYS U 240 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 248 through 257
      removed outlier: 4.183A  pdb=" N   ILE U 254 " --> pdb=" O   PRO U 250 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLY U 255 " --> pdb=" O   LEU U 251 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 258 through 263
    Processing helix  chain 'U' and resid 266 through 275
      removed outlier: 3.567A  pdb=" N   LEU U 271 " --> pdb=" O   THR U 267 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LYS U 272 " --> pdb=" O   ASP U 268 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA U 275 " --> pdb=" O   LEU U 271 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 277 through 282
      removed outlier: 3.706A  pdb=" N   ASP U 282 " --> pdb=" O   GLY U 278 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 287 through 294
      removed outlier: 3.678A  pdb=" N   VAL U 291 " --> pdb=" O   SER U 287 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA U 293 " --> pdb=" O   ARG U 289 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE U 294 " --> pdb=" O   THR U 290 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 308 through 312
      removed outlier: 3.684A  pdb=" N   ALA U 311 " --> pdb=" O   LEU U 308 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 320 through 325
    Processing helix  chain 'U' and resid 329 through 334
      removed outlier: 3.919A  pdb=" N   PHE U 334 " --> pdb=" O   TRP U 330 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 335 through 344
      removed outlier: 3.978A  pdb=" N   LEU U 339 " --> pdb=" O   LEU U 335 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 363 through 376
      removed outlier: 3.621A  pdb=" N   ILE U 367 " --> pdb=" O   PHE U 363 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY U 369 " --> pdb=" O   SER U 365 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   LEU U 373 " --> pdb=" O   GLY U 369 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLY U 374 " --> pdb=" O   ALA U 370 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 377 through 386
      removed outlier: 4.929A  pdb=" N   PHE U 383 " --> pdb=" O   CYS U 379 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ALA U 384 " --> pdb=" O   LEU U 380 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 392 through 397
      removed outlier: 3.716A  pdb=" N   THR U 396 " --> pdb=" O   SER U 392 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 462 through 467
    Processing helix  chain 'U' and resid 490 through 495
    Processing helix  chain 'U' and resid 525 through 535
      removed outlier: 3.749A  pdb=" N   GLN U 530 " --> pdb=" O   GLU U 526 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 540 through 544
      removed outlier: 3.508A  pdb=" N   LEU U 544 " --> pdb=" O   ILE U 541 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 563 through 575
      removed outlier: 3.615A  pdb=" N   ALA U 570 " --> pdb=" O   ARG U 566 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG U 575 " --> pdb=" O   ARG U 571 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 593 through 603
      removed outlier: 3.766A  pdb=" N   VAL U 597 " --> pdb=" O   SER U 593 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL U 600 " --> pdb=" O   MET U 596 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 652 through 656
    Processing helix  chain 'U' and resid 700 through 704
      removed outlier: 3.660A  pdb=" N   SER U 704 " --> pdb=" O   SER U 701 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 742 through 747
    Processing helix  chain 'U' and resid 748 through 752
    Processing helix  chain 'U' and resid 775 through 780
      removed outlier: 3.556A  pdb=" N   LEU U 780 " --> pdb=" O   PHE U 776 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 789 through 802
      removed outlier: 3.621A  pdb=" N   ILE U 795 " --> pdb=" O   GLN U 791 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN U 796 " --> pdb=" O   ARG U 792 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS U 799 " --> pdb=" O   ILE U 795 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 803 through 806
    Processing helix  chain 'U' and resid 828 through 833
      removed outlier: 3.685A  pdb=" N   LYS U 833 " --> pdb=" O   LYS U 829 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 834 through 836
      No H-bonds generated for 'chain 'U' and resid 834 through 836'
    Processing helix  chain 'U' and resid 838 through 842
      removed outlier: 3.983A  pdb=" N   GLN U 842 " --> pdb=" O   MET U 839 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 843 through 847
      removed outlier: 4.072A  pdb=" N   TRP U 846 " --> pdb=" O   ASP U 843 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 875 through 881
    Processing helix  chain 'U' and resid 885 through 897
      removed outlier: 3.825A  pdb=" N   ALA U 889 " --> pdb=" O   ASN U 885 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE U 891 " --> pdb=" O   THR U 887 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE U 894 " --> pdb=" O   MET U 890 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   PHE U 896 " --> pdb=" O   ILE U 892 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER U 897 " --> pdb=" O   ALA U 893 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 904 through 907
    Processing helix  chain 'U' and resid 908 through 913
    Processing helix  chain 'U' and resid 925 through 930
      removed outlier: 3.774A  pdb=" N   LYS U 930 " --> pdb=" O   ALA U 926 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 935 through 940
    Processing helix  chain 'U' and resid 940 through 945
      removed outlier: 3.555A  pdb=" N   SER U 945 " --> pdb=" O   ASN U 941 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 946 through 951
    Processing helix  chain 'U' and resid 956 through 962
    Processing helix  chain 'U' and resid 994 through 1007
      removed outlier: 3.639A  pdb=" N   SER U 999 " --> pdb=" O   ALA U 995 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR U1000 " --> pdb=" O   ASN U 996 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG U1001 " --> pdb=" O   SER U 997 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1013 through 1015
      No H-bonds generated for 'chain 'U' and resid 1013 through 1015'
    Processing helix  chain 'U' and resid 1016 through 1021
      removed outlier: 3.614A  pdb=" N   ILE U1021 " --> pdb=" O   VAL U1017 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1031 through 1035
      removed outlier: 3.917A  pdb=" N   PHE U1035 " --> pdb=" O   GLY U1032 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1037 through 1043
      removed outlier: 3.558A  pdb=" N   TYR U1041 " --> pdb=" O   TYR U1037 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA U1042 " --> pdb=" O   THR U1038 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS U1043 " --> pdb=" O   PRO U1039 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 1037 through 1043'
    Processing helix  chain 'U' and resid 1048 through 1053
      removed outlier: 3.843A  pdb=" N   PHE U1052 " --> pdb=" O   ALA U1048 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1120 through 1125
      removed outlier: 3.553A  pdb=" N   GLN U1124 " --> pdb=" O   SER U1120 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1148 through 1153
      removed outlier: 3.509A  pdb=" N   LEU U1152 " --> pdb=" O   ASN U1148 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1171 through 1176
      removed outlier: 3.714A  pdb=" N   LYS U1175 " --> pdb=" O   MET U1171 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1185 through 1191
      removed outlier: 4.306A  pdb=" N   ILE U1189 " --> pdb=" O   MET U1185 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA U1190 " --> pdb=" O   GLU U1186 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1200 through 1204
      removed outlier: 3.822A  pdb=" N   LEU U1204 " --> pdb=" O   VAL U1201 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1220 through 1223
    Processing helix  chain 'U' and resid 1224 through 1233
      removed outlier: 3.830A  pdb=" N   ALA U1228 " --> pdb=" O   LYS U1224 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1250 through 1264
      removed outlier: 3.537A  pdb=" N   VAL U1257 " --> pdb=" O   SER U1253 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL U1259 " --> pdb=" O   LYS U1255 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA U1260 " --> pdb=" O   THR U1256 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1308 through 1314
      removed outlier: 3.519A  pdb=" N   LYS U1312 " --> pdb=" O   GLY U1308 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU U1313 " --> pdb=" O   ALA U1309 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'U' and resid 438 through 445
      removed outlier: 6.806A  pdb=" N   ASN U 439 " --> pdb=" O   THR U 426 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   THR U 426 " --> pdb=" O   ASN U 439 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   LEU U 441 " --> pdb=" O   ASN U 424 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN U 424 " --> pdb=" O   LEU U 441 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE U 420 " --> pdb=" O   ILE U 445 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'U' and resid 450 through 451
      removed outlier: 6.175A  pdb=" N   THR U 451 " --> pdb=" O   SER U 612 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   LEU U 580 " --> pdb=" O   ILE U 611 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   VAL U 613 " --> pdb=" O   LEU U 580 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   LEU U 582 " --> pdb=" O   VAL U 613 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'U' and resid 1079 through 1080
    Processing sheet with id=AA4, first strand: chain 'U' and resid 1156 through 1159
      removed outlier: 6.714A  pdb=" N   GLY U1157 " --> pdb=" O   LEU U1241 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    158 hydrogen bonds defined for protein.
    420 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: 2.64

  Time building geometry restraints manager: 4.15 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2048
        1.33 -     1.45: 2223
        1.45 -     1.57: 5402
        1.57 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 9761
  Sorted by residual:
  bond pdb=" C   GLN U  76 "
       pdb=" N   PRO U  77 "
    ideal  model  delta    sigma   weight residual
    1.333  1.378 -0.045 7.80e-03 1.64e+04 3.37e+01
  bond pdb=" CG1 ILE U 171 "
       pdb=" CD1 ILE U 171 "
    ideal  model  delta    sigma   weight residual
    1.513  1.363  0.150 3.90e-02 6.57e+02 1.49e+01
  bond pdb=" CB  VAL U1024 "
       pdb=" CG2 VAL U1024 "
    ideal  model  delta    sigma   weight residual
    1.521  1.421  0.100 3.30e-02 9.18e+02 9.18e+00
  bond pdb=" CG  ARG U 175 "
       pdb=" CD  ARG U 175 "
    ideal  model  delta    sigma   weight residual
    1.520  1.445  0.075 3.00e-02 1.11e+03 6.22e+00
  bond pdb=" CB  ILE U 160 "
       pdb=" CG2 ILE U 160 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.66e+00
  ... (remaining 9756 not shown)

  Histogram of bond angle deviations from ideal:
       97.33 -   104.71: 145
      104.71 -   112.08: 4357
      112.08 -   119.46: 3782
      119.46 -   126.83: 4806
      126.83 -   134.20: 109
  Bond angle restraints: 13199
  Sorted by residual:
  angle pdb=" N   ILE U1170 "
        pdb=" CA  ILE U1170 "
        pdb=" C   ILE U1170 "
      ideal   model   delta    sigma   weight residual
     112.83  104.69    8.14 9.90e-01 1.02e+00 6.75e+01
  angle pdb=" N   ILE U 213 "
        pdb=" CA  ILE U 213 "
        pdb=" C   ILE U 213 "
      ideal   model   delta    sigma   weight residual
     113.71  107.32    6.39 9.50e-01 1.11e+00 4.53e+01
  angle pdb=" N   LEU U  67 "
        pdb=" CA  LEU U  67 "
        pdb=" C   LEU U  67 "
      ideal   model   delta    sigma   weight residual
     113.38  105.94    7.44 1.23e+00 6.61e-01 3.66e+01
  angle pdb=" C   ASN U 946 "
        pdb=" N   ILE U 947 "
        pdb=" CA  ILE U 947 "
      ideal   model   delta    sigma   weight residual
     120.53  127.26   -6.73 1.41e+00 5.03e-01 2.28e+01
  angle pdb=" N   GLY U 924 "
        pdb=" CA  GLY U 924 "
        pdb=" C   GLY U 924 "
      ideal   model   delta    sigma   weight residual
     115.46  107.75    7.71 1.63e+00 3.76e-01 2.24e+01
  ... (remaining 13194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 5279
       16.28 -    32.56: 428
       32.56 -    48.84: 99
       48.84 -    65.12: 10
       65.12 -    81.40: 7
  Dihedral angle restraints: 5823
    sinusoidal: 2288
      harmonic: 3535
  Sorted by residual:
  dihedral pdb=" CA  LEU U 712 "
           pdb=" C   LEU U 712 "
           pdb=" N   ALA U 713 "
           pdb=" CA  ALA U 713 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.33   44.67     0      5.00e+00 4.00e-02 7.98e+01
  dihedral pdb=" CA  TYR U1037 "
           pdb=" C   TYR U1037 "
           pdb=" N   THR U1038 "
           pdb=" CA  THR U1038 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.24  -37.76     0      5.00e+00 4.00e-02 5.70e+01
  dihedral pdb=" CA  ILE U1271 "
           pdb=" C   ILE U1271 "
           pdb=" N   VAL U1272 "
           pdb=" CA  VAL U1272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.00  -34.00     0      5.00e+00 4.00e-02 4.62e+01
  ... (remaining 5820 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1305
       0.093 -    0.187: 177
       0.187 -    0.280: 16
       0.280 -    0.374: 3
       0.374 -    0.467: 1
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CB  ILE U 785 "
            pdb=" CA  ILE U 785 "
            pdb=" CG1 ILE U 785 "
            pdb=" CG2 ILE U 785 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CB  VAL U 808 "
            pdb=" CA  VAL U 808 "
            pdb=" CG1 VAL U 808 "
            pdb=" CG2 VAL U 808 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CB  VAL U 360 "
            pdb=" CA  VAL U 360 "
            pdb=" CG1 VAL U 360 "
            pdb=" CG2 VAL U 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS U 969 "    0.060 5.00e-02 4.00e+02   8.99e-02 1.29e+01
        pdb=" N   PRO U 970 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO U 970 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO U 970 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE U 383 "   -0.023 2.00e-02 2.50e+03   2.06e-02 7.44e+00
        pdb=" CG  PHE U 383 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE U 383 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE U 383 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE U 383 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE U 383 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE U 383 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER U 249 "   -0.044 5.00e-02 4.00e+02   6.62e-02 7.01e+00
        pdb=" N   PRO U 250 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO U 250 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO U 250 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2970
        2.81 -     3.33: 8225
        3.33 -     3.86: 14900
        3.86 -     4.38: 17263
        4.38 -     4.90: 29290
  Nonbonded interactions: 72648
  Sorted by model distance:
  nonbonded pdb=" O   GLN U 546 "
            pdb=" OG1 THR U 550 "
     model   vdw
     2.291 2.440
  nonbonded pdb=" OG1 THR U 227 "
            pdb=" O   GLY U 369 "
     model   vdw
     2.295 2.440
  nonbonded pdb=" O   SER U1027 "
            pdb=" OG  SER U1027 "
     model   vdw
     2.308 2.440
  nonbonded pdb=" O   GLN U1196 "
            pdb=" NH2 ARG U1226 "
     model   vdw
     2.316 2.520
  nonbonded pdb=" O   THR U 155 "
            pdb=" OG1 THR U 155 "
     model   vdw
     2.330 2.440
  ... (remaining 72643 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6129      2.51       5
     N    1627      2.21       5
     O    1766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  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:          3.020
  Check model and map are aligned:         0.170
  Convert atoms to be neutral:             0.100
  Process input model:                     28.630
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
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      :  0.011   0.150   9761  Z= 0.698
  Angle     :  1.380  14.085  13199  Z= 0.753
  Chirality :  0.066   0.467   1502
  Planarity :  0.007   0.090   1689
  Dihedral  : 13.072  81.405   3551
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.03 %
    Favored  : 88.89 %
  Rotamer Outliers :  0.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

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: -6.35 (0.16), residues: 1224
  helix: -4.96 (0.08), residues: 637
  sheet: -3.98 (0.66), residues: 36
  loop : -3.12 (0.23), residues: 551

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 208
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 214
  average time/residue: 0.2416
  time to fit residues: 69.8108
Evaluate side-chains
  125 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 1.179 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0887
  time to fit residues: 1.8885
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 93 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 96 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 111 optimal weight:    9.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 170 GLN
U 207 ASN
U 466 GLN
U 492 GLN
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 536 ASN
U 546 GLN
U 576 ASN
U 605 GLN
U 640 HIS
U 697 GLN
U 708 HIS
U 778 GLN
U 791 GLN
U 842 GLN
U 875 GLN
** U 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U1097 ASN
** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9761  Z= 0.229
  Angle     :  0.763  16.240  13199  Z= 0.389
  Chirality :  0.044   0.234   1502
  Planarity :  0.005   0.073   1689
  Dihedral  :  7.031  38.493   1327
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.58 %
    Favored  : 91.34 %
  Rotamer Outliers :  3.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.50 (0.19), residues: 1224
  helix: -4.36 (0.12), residues: 637
  sheet: -3.27 (0.70), residues: 36
  loop : -2.59 (0.25), residues: 551

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 35
  outliers final: 11
  residues processed: 167
  average time/residue: 0.1960
  time to fit residues: 48.1133
Evaluate side-chains
  125 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.182 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0898
  time to fit residues: 3.3584
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 111 optimal weight:    9.9990
   chunk 120 optimal weight:   30.0000
   chunk 99 optimal weight:    0.0970
   chunk 110 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U1124 GLN
U1258 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9761  Z= 0.192
  Angle     :  0.688   9.511  13199  Z= 0.348
  Chirality :  0.043   0.159   1502
  Planarity :  0.005   0.094   1689
  Dihedral  :  6.237  35.812   1327
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer Outliers :  2.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.14 (0.19), residues: 1224
  helix: -3.93 (0.14), residues: 658
  sheet: -2.51 (0.68), residues: 43
  loop : -2.55 (0.25), residues: 523

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 8
  residues processed: 150
  average time/residue: 0.1919
  time to fit residues: 42.1412
Evaluate side-chains
  114 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 1.141 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0959
  time to fit residues: 2.9628
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 12 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0170
   chunk 118 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   overall best weight:    2.2622

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 546 GLN
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U1258 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.102   9761  Z= 0.370
  Angle     :  0.756  12.059  13199  Z= 0.375
  Chirality :  0.046   0.162   1502
  Planarity :  0.005   0.102   1689
  Dihedral  :  6.458  38.725   1327
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer Outliers :  4.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -4.87 (0.21), residues: 1224
  helix: -3.80 (0.15), residues: 658
  sheet: -2.11 (0.72), residues: 43
  loop : -2.31 (0.27), residues: 523

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 116
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 42
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1921
  time to fit residues: 42.3100
Evaluate side-chains
  122 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.207 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0917
  time to fit residues: 3.9981
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 101 optimal weight:   50.0000
   chunk 82 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 60 optimal weight:   30.0000
   chunk 106 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U1258 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.134   9761  Z= 0.201
  Angle     :  0.672   9.431  13199  Z= 0.334
  Chirality :  0.043   0.172   1502
  Planarity :  0.005   0.105   1689
  Dihedral  :  5.893  35.916   1327
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer Outliers :  1.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -4.62 (0.21), residues: 1224
  helix: -3.60 (0.15), residues: 660
  sheet: -1.75 (0.76), residues: 43
  loop : -2.22 (0.27), residues: 521

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 6
  residues processed: 130
  average time/residue: 0.1965
  time to fit residues: 37.5344
Evaluate side-chains
  115 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 1.104 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0951
  time to fit residues: 2.6180
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 107 optimal weight:    0.0870
   chunk 23 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 119 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 55 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0670
   chunk 39 optimal weight:    7.9990
   chunk 62 optimal weight:    0.3980
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 466 GLN
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 765 ASN
U1258 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9761  Z= 0.169
  Angle     :  0.634   8.606  13199  Z= 0.312
  Chirality :  0.042   0.170   1502
  Planarity :  0.004   0.106   1689
  Dihedral  :  5.518  33.482   1327
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer Outliers :  1.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 (0.21), residues: 1224
  helix: -3.41 (0.15), residues: 679
  sheet: -1.72 (0.75), residues: 43
  loop : -2.17 (0.27), residues: 502

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 5
  residues processed: 131
  average time/residue: 0.2103
  time to fit residues: 39.3227
Evaluate side-chains
  114 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 1.094 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0906
  time to fit residues: 2.4197
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0870
   chunk 86 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 118 optimal weight:   10.0000
   chunk 74 optimal weight:    0.3980
   chunk 72 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.2162

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 375 ASN
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.239   9761  Z= 0.254
  Angle     :  0.682  15.186  13199  Z= 0.341
  Chirality :  0.043   0.154   1502
  Planarity :  0.006   0.127   1689
  Dihedral  :  5.552  34.397   1327
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer Outliers :  1.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -4.28 (0.21), residues: 1224
  helix: -3.27 (0.16), residues: 676
  sheet: -1.21 (0.79), residues: 41
  loop : -2.10 (0.27), residues: 507

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 5
  residues processed: 125
  average time/residue: 0.2275
  time to fit residues: 41.1627
Evaluate side-chains
  115 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 1.225 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0922
  time to fit residues: 2.5478
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0970
   chunk 93 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9761  Z= 0.179
  Angle     :  0.648  11.691  13199  Z= 0.317
  Chirality :  0.042   0.179   1502
  Planarity :  0.005   0.107   1689
  Dihedral  :  5.280  32.941   1327
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer Outliers :  0.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -4.10 (0.22), residues: 1224
  helix: -3.12 (0.16), residues: 682
  sheet: -0.70 (0.86), residues: 36
  loop : -2.06 (0.27), residues: 506

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 122
  average time/residue: 0.2005
  time to fit residues: 35.5909
Evaluate side-chains
  113 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 1.107 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0834
  time to fit residues: 2.2629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 110 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 99 optimal weight:   20.0000
   chunk 104 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 442 ASN
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.070   9761  Z= 0.389
  Angle     :  0.745  12.907  13199  Z= 0.362
  Chirality :  0.047   0.203   1502
  Planarity :  0.006   0.118   1689
  Dihedral  :  5.798  36.953   1327
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer Outliers :  0.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -4.12 (0.22), residues: 1224
  helix: -3.17 (0.16), residues: 674
  sheet: -0.95 (0.80), residues: 41
  loop : -2.02 (0.28), residues: 509

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 115
  average time/residue: 0.2220
  time to fit residues: 36.9358
Evaluate side-chains
  106 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.205 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0911
  time to fit residues: 2.0331
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 122 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U1258 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.093   9761  Z= 0.190
  Angle     :  0.690  11.205  13199  Z= 0.334
  Chirality :  0.043   0.200   1502
  Planarity :  0.005   0.118   1689
  Dihedral  :  5.340  34.045   1327
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.03 %
    Favored  : 92.89 %
  Rotamer Outliers :  0.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.98 (0.22), residues: 1224
  helix: -3.03 (0.17), residues: 685
  sheet: -0.77 (0.81), residues: 41
  loop : -1.95 (0.28), residues: 498

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 118
  average time/residue: 0.2101
  time to fit residues: 36.0087
Evaluate side-chains
  108 residues out of total 1026 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 1.129 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0929
  time to fit residues: 1.9211
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U1258 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.219199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.176605 restraints weight = 10821.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.171816 restraints weight = 19549.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.167032 restraints weight = 18076.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.4673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.010   0.746   9761  Z= 0.462
  Angle     :  1.255 106.098  13199  Z= 0.521
  Chirality :  0.045   0.399   1502
  Planarity :  0.005   0.106   1689
  Dihedral  :  5.359  33.921   1327
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.94 %
    Favored  : 92.97 %
  Rotamer Outliers :  0.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.96 (0.22), residues: 1224
  helix: -3.02 (0.17), residues: 681
  sheet: -0.78 (0.81), residues: 41
  loop : -1.96 (0.28), residues: 502

===============================================================================
Job complete
usr+sys time: 1886.63 seconds
wall clock time: 35 minutes 1.22 seconds (2101.22 seconds total)