Starting phenix.real_space_refine (version: dev)
on Fri May 13 02:30:04 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_0956/05_2022/6lr0_0956.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_0956/05_2022/6lr0_0956.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_0956/05_2022/6lr0_0956.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_0956/05_2022/6lr0_0956.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_0956/05_2022/6lr0_0956.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_0956/05_2022/6lr0_0956.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=  -0.000 sd=   0.008
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 TYR 1037": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR 1310": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib"
  Total number of atoms: 9587
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "U"
      Number of atoms: 9587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1232, 9587
          Classifications: {'peptide': 1232}
          Link IDs: {'PTRANS': 34, 'TRANS': 1197}
          Chain breaks: 2
  Time building chain proxies: 6.10, per 1000 atoms: 0.64
  Number of scatterers: 9587
  At special positions: 0
  Unit cell: (96.46, 157.94, 103.88, 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      55     16.00
     O    1777      8.00
     N    1623      7.00
     C    6132      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: 3.26
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2270

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 3 sheets defined
      43.0% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'U' and resid 5 through 14
      removed outlier: 3.639A  pdb=" N   ILE U  10 " --> pdb=" O   ILE U   6 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS U  11 " --> pdb=" O   LEU U   7 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS U  12 " --> pdb=" O   ARG U   8 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE U  13 " --> pdb=" O   SER U   9 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 46 through 50
    Processing helix  chain 'U' and resid 55 through 60
      removed outlier: 3.552A  pdb=" N   TRP U  60 " --> pdb=" O   SER U  56 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 60 through 65
      removed outlier: 3.658A  pdb=" N   GLY U  65 " --> pdb=" O   LEU U  61 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 67 through 75
    Processing helix  chain 'U' and resid 79 through 84
    Processing helix  chain 'U' and resid 86 through 102
      removed outlier: 3.809A  pdb=" N   ILE U  91 " --> pdb=" O   THR U  87 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU U  96 " --> pdb=" O   ASP U  92 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLU U  99 " --> pdb=" O   VAL U  95 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 145 through 156
      removed outlier: 4.177A  pdb=" N   ALA U 151 " --> pdb=" O   GLY U 147 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE U 154 " --> pdb=" O   VAL U 150 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 156 through 162
      removed outlier: 3.728A  pdb=" N   ILE U 160 " --> pdb=" O   GLY U 156 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE U 162 " --> pdb=" O   ILE U 158 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 167 through 183
      removed outlier: 3.633A  pdb=" N   GLN U 172 " --> pdb=" O   ALA U 168 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LYS U 173 " --> pdb=" O   ARG U 169 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LYS U 176 " --> pdb=" O   GLN U 172 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 188 through 192
    Processing helix  chain 'U' and resid 194 through 202
      removed outlier: 4.013A  pdb=" N   THR U 200 " --> pdb=" O   GLY U 196 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE U 202 " --> pdb=" O   LEU U 198 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 206 through 214
      removed outlier: 3.612A  pdb=" N   ASP U 211 " --> pdb=" O   ASN U 207 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ALA U 212 " --> pdb=" O   LYS U 208 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA U 214 " --> pdb=" O   ASN U 210 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 214 through 219
      removed outlier: 4.001A  pdb=" N   ALA U 218 " --> pdb=" O   ALA U 214 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 233 through 238
      removed outlier: 4.227A  pdb=" N   ARG U 237 " --> pdb=" O   LEU U 233 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY U 238 " --> pdb=" O   GLY U 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 233 through 238'
    Processing helix  chain 'U' and resid 240 through 245
      removed outlier: 3.704A  pdb=" N   VAL U 244 " --> pdb=" O   LYS U 240 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE U 245 " --> pdb=" O   LEU U 241 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 240 through 245'
    Processing helix  chain 'U' and resid 248 through 253
    Processing helix  chain 'U' and resid 263 through 267
      removed outlier: 3.578A  pdb=" N   THR U 267 " --> pdb=" O   SER U 264 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 273 through 277
      removed outlier: 3.579A  pdb=" N   LYS U 276 " --> pdb=" O   ALA U 273 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 287 through 292
      removed outlier: 3.628A  pdb=" N   VAL U 291 " --> pdb=" O   SER U 287 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 293 through 295
      No H-bonds generated for 'chain 'U' and resid 293 through 295'
    Processing helix  chain 'U' and resid 301 through 305
      removed outlier: 3.583A  pdb=" N   GLU U 305 " --> pdb=" O   GLU U 302 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 309 through 317
      removed outlier: 4.084A  pdb=" N   TRP U 314 " --> pdb=" O   PHE U 310 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY U 315 " --> pdb=" O   ALA U 311 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 320 through 325
    Processing helix  chain 'U' and resid 325 through 344
      removed outlier: 3.591A  pdb=" N   VAL U 329 " --> pdb=" O   PHE U 325 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS U 331 " --> pdb=" O   GLY U 327 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   PHE U 334 " --> pdb=" O   TRP U 330 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA U 338 " --> pdb=" O   PHE U 334 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 356 through 361
      removed outlier: 3.912A  pdb=" N   VAL U 360 " --> pdb=" O   PRO U 356 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 363 through 375
      removed outlier: 3.640A  pdb=" N   ILE U 367 " --> pdb=" O   PHE U 363 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LEU U 373 " --> pdb=" O   GLY U 369 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 377 through 382
      removed outlier: 3.751A  pdb=" N   ALA U 382 " --> pdb=" O   PRO U 378 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 382 through 387
    Processing helix  chain 'U' and resid 392 through 397
      removed outlier: 3.720A  pdb=" N   THR U 396 " --> pdb=" O   SER U 392 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 462 through 467
      removed outlier: 3.825A  pdb=" N   LEU U 467 " --> pdb=" O   THR U 463 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 490 through 495
    Processing helix  chain 'U' and resid 525 through 532
      removed outlier: 3.555A  pdb=" N   VAL U 529 " --> pdb=" O   MET U 525 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN U 530 " --> pdb=" O   GLU U 526 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 562 through 575
      removed outlier: 3.840A  pdb=" N   ARG U 566 " --> pdb=" O   GLY U 562 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA U 570 " --> pdb=" O   ARG U 566 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ARG U 575 " --> pdb=" O   ARG U 571 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 595 through 603
      removed outlier: 3.986A  pdb=" N   GLU U 599 " --> pdb=" O   ALA U 595 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL U 600 " --> pdb=" O   MET U 596 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU U 601 " --> pdb=" O   VAL U 597 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS U 603 " --> pdb=" O   GLU U 599 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 616 through 621
      removed outlier: 4.317A  pdb=" N   VAL U 620 " --> pdb=" O   ARG U 616 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 639 through 645
      removed outlier: 4.545A  pdb=" N   GLU U 645 " --> pdb=" O   GLU U 641 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 740 through 748
      removed outlier: 4.054A  pdb=" N   ILE U 744 " --> pdb=" O   PRO U 740 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS U 746 " --> pdb=" O   ARG U 742 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 756 through 761
    Processing helix  chain 'U' and resid 768 through 780
      removed outlier: 3.577A  pdb=" N   ALA U 773 " --> pdb=" O   THR U 769 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE U 774 " --> pdb=" O   PRO U 770 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE U 779 " --> pdb=" O   LEU U 775 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 789 through 808
      removed outlier: 3.689A  pdb=" N   ASN U 796 " --> pdb=" O   ARG U 792 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL U 798 " --> pdb=" O   GLN U 794 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   VAL U 803 " --> pdb=" O   CYS U 799 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA U 804 " --> pdb=" O   LEU U 800 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   MET U 805 " --> pdb=" O   LEU U 801 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 810 through 819
      removed outlier: 3.794A  pdb=" N   GLN U 816 " --> pdb=" O   THR U 812 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA U 819 " --> pdb=" O   LEU U 815 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 827 through 837
      removed outlier: 3.936A  pdb=" N   LYS U 833 " --> pdb=" O   LYS U 829 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE U 834 " --> pdb=" O   ARG U 830 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG U 837 " --> pdb=" O   LYS U 833 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 857 through 862
    Processing helix  chain 'U' and resid 867 through 871
      removed outlier: 3.880A  pdb=" N   GLY U 870 " --> pdb=" O   GLN U 867 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 875 through 880
    Processing helix  chain 'U' and resid 888 through 895
    Processing helix  chain 'U' and resid 903 through 907
      removed outlier: 3.605A  pdb=" N   CYS U 906 " --> pdb=" O   VAL U 903 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 908 through 913
    Processing helix  chain 'U' and resid 925 through 931
      removed outlier: 3.726A  pdb=" N   GLN U 931 " --> pdb=" O   SER U 927 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 935 through 943
      removed outlier: 3.678A  pdb=" N   ILE U 939 " --> pdb=" O   MET U 935 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ASN U 941 " --> pdb=" O   GLY U 937 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU U 942 " --> pdb=" O   GLN U 938 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 946 through 954
      removed outlier: 3.712A  pdb=" N   VAL U 950 " --> pdb=" O   ASN U 946 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLY U 952 " --> pdb=" O   ARG U 948 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 968 through 976
      removed outlier: 4.472A  pdb=" N   ALA U 974 " --> pdb=" O   PRO U 970 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLN U 976 " --> pdb=" O   LYS U 972 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 976 through 981
      removed outlier: 3.560A  pdb=" N   ILE U 980 " --> pdb=" O   GLN U 976 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 981 through 989
      removed outlier: 3.505A  pdb=" N   PHE U 987 " --> pdb=" O   PHE U 983 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA U 988 " --> pdb=" O   CYS U 984 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 991 through 1007
      removed outlier: 3.847A  pdb=" N   TYR U1000 " --> pdb=" O   ASN U 996 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ARG U1001 " --> pdb=" O   SER U 997 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1014 through 1021
      removed outlier: 3.725A  pdb=" N   PHE U1018 " --> pdb=" O   PHE U1014 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1048 through 1056
      removed outlier: 3.837A  pdb=" N   PHE U1052 " --> pdb=" O   ALA U1048 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLN U1053 " --> pdb=" O   ALA U1049 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU U1054 " --> pdb=" O   ARG U1050 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1120 through 1125
      removed outlier: 3.802A  pdb=" N   GLN U1124 " --> pdb=" O   SER U1120 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1148 through 1153
      removed outlier: 3.636A  pdb=" N   LEU U1152 " --> pdb=" O   ASN U1148 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1171 through 1176
    Processing helix  chain 'U' and resid 1224 through 1233
      removed outlier: 4.102A  pdb=" N   ALA U1228 " --> pdb=" O   LYS U1224 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1250 through 1262
      removed outlier: 3.792A  pdb=" N   THR U1256 " --> pdb=" O   GLU U1252 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL U1257 " --> pdb=" O   SER U1253 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL U1259 " --> pdb=" O   LYS U1255 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1308 through 1314
    Processing sheet with id=AA1, first strand: chain 'U' and resid 439 through 445
      removed outlier: 6.888A  pdb=" N   ASN U 439 " --> pdb=" O   THR U 426 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   THR U 426 " --> pdb=" O   ASN U 439 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   LEU U 441 " --> pdb=" O   ASN U 424 " (cutoff:3.500A)
      removed outlier: 3.559A  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 453
      removed outlier: 6.251A  pdb=" N   THR U 451 " --> pdb=" O   SER U 612 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU U 580 " --> pdb=" O   ILE U 611 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   VAL U 613 " --> pdb=" O   LEU U 580 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LEU U 582 " --> pdb=" O   VAL U 613 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLY U 499 " --> pdb=" O   LEU U 581 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'U' and resid 1156 through 1159
      removed outlier: 6.321A  pdb=" N   GLY U1157 " --> pdb=" O   LEU U1241 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    195 hydrogen bonds defined for protein.
    558 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: 2.68

  Time building geometry restraints manager: 3.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2715
        1.33 -     1.45: 1765
        1.45 -     1.57: 5199
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 9769
  Sorted by residual:
  bond pdb=" C   TRP U 752 "
       pdb=" N   PRO U 753 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.050 8.40e-03 1.42e+04 3.49e+01
  bond pdb=" CG1 ILE U 947 "
       pdb=" CD1 ILE U 947 "
    ideal  model  delta    sigma   weight residual
    1.513  1.385  0.128 3.90e-02 6.57e+02 1.07e+01
  bond pdb=" CG1 ILE U 171 "
       pdb=" CD1 ILE U 171 "
    ideal  model  delta    sigma   weight residual
    1.513  1.403  0.110 3.90e-02 6.57e+02 7.92e+00
  bond pdb=" CB  VAL U 936 "
       pdb=" CG1 VAL U 936 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.57e+00
  bond pdb=" CB  VAL U1024 "
       pdb=" CG1 VAL U1024 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.44e+00
  ... (remaining 9764 not shown)

  Histogram of bond angle deviations from ideal:
       97.51 -   104.91: 140
      104.91 -   112.31: 4452
      112.31 -   119.72: 3940
      119.72 -   127.12: 4580
      127.12 -   134.52: 89
  Bond angle restraints: 13201
  Sorted by residual:
  angle pdb=" CA  LEU U 219 "
        pdb=" CB  LEU U 219 "
        pdb=" CG  LEU U 219 "
      ideal   model   delta    sigma   weight residual
     116.30  133.61  -17.31 3.50e+00 8.16e-02 2.45e+01
  angle pdb=" N   SER U1104 "
        pdb=" CA  SER U1104 "
        pdb=" C   SER U1104 "
      ideal   model   delta    sigma   weight residual
     109.58  101.95    7.63 1.63e+00 3.76e-01 2.19e+01
  angle pdb=" C   ASP U 849 "
        pdb=" N   LEU U 850 "
        pdb=" CA  LEU U 850 "
      ideal   model   delta    sigma   weight residual
     121.54  130.47   -8.93 1.91e+00 2.74e-01 2.18e+01
  angle pdb=" CA  LEU U1026 "
        pdb=" CB  LEU U1026 "
        pdb=" CG  LEU U1026 "
      ideal   model   delta    sigma   weight residual
     116.30  131.48  -15.18 3.50e+00 8.16e-02 1.88e+01
  angle pdb=" N   GLY U1076 "
        pdb=" CA  GLY U1076 "
        pdb=" C   GLY U1076 "
      ideal   model   delta    sigma   weight residual
     113.18  122.89   -9.71 2.37e+00 1.78e-01 1.68e+01
  ... (remaining 13196 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.74: 5235
       15.74 -    31.48: 456
       31.48 -    47.23: 116
       47.23 -    62.97: 10
       62.97 -    78.71: 9
  Dihedral angle restraints: 5826
    sinusoidal: 2293
      harmonic: 3533
  Sorted by residual:
  dihedral pdb=" CA  THR U 510 "
           pdb=" C   THR U 510 "
           pdb=" N   THR U 511 "
           pdb=" CA  THR U 511 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -129.97  -50.03     0      5.00e+00 4.00e-02 1.00e+02
  dihedral pdb=" CA  PHE U 540 "
           pdb=" C   PHE U 540 "
           pdb=" N   ILE U 541 "
           pdb=" CA  ILE U 541 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.57  -33.43     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  VAL U 635 "
           pdb=" C   VAL U 635 "
           pdb=" N   GLU U 636 "
           pdb=" CA  GLU U 636 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.79   31.21     0      5.00e+00 4.00e-02 3.90e+01
  ... (remaining 5823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1307
       0.091 -    0.183: 172
       0.183 -    0.274: 18
       0.274 -    0.366: 0
       0.366 -    0.457: 1
  Chirality restraints: 1498
  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    2.19    0.46 2.00e-01 2.50e+01 5.22e+00
  chirality pdb=" CB  ILE U1078 "
            pdb=" CA  ILE U1078 "
            pdb=" CG1 ILE U1078 "
            pdb=" CG2 ILE U1078 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CB  VAL U 279 "
            pdb=" CA  VAL U 279 "
            pdb=" CG1 VAL U 279 "
            pdb=" CG2 VAL U 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1495 not shown)

  Planarity restraints: 1692
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR U 769 "   -0.050 5.00e-02 4.00e+02   7.49e-02 8.98e+00
        pdb=" N   PRO U 770 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO U 770 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO U 770 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS U 969 "   -0.045 5.00e-02 4.00e+02   6.70e-02 7.17e+00
        pdb=" N   PRO U 970 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO U 970 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO U 970 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE U 171 "    0.013 2.00e-02 2.50e+03   2.64e-02 6.98e+00
        pdb=" C   ILE U 171 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ILE U 171 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN U 172 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1689 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1829
        2.76 -     3.30: 8529
        3.30 -     3.83: 14947
        3.83 -     4.37: 17490
        4.37 -     4.90: 29554
  Nonbonded interactions: 72349
  Sorted by model distance:
  nonbonded pdb=" OG1 THR U 511 "
            pdb=" O   THR U 550 "
     model   vdw
     2.228 2.440
  nonbonded pdb=" NH2 ARG U 575 "
            pdb=" O   ILE U 953 "
     model   vdw
     2.290 2.520
  nonbonded pdb=" OG1 THR U 227 "
            pdb=" O   GLY U 369 "
     model   vdw
     2.292 2.440
  nonbonded pdb=" O   GLN U1196 "
            pdb=" NH2 ARG U1226 "
     model   vdw
     2.325 2.520
  nonbonded pdb=" O   GLY U 638 "
            pdb=" OH  TYR U 650 "
     model   vdw
     2.336 2.440
  ... (remaining 72344 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      55      5.16       5
     C    6132      2.51       5
     N    1623      2.21       5
     O    1777      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:             1.260
  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:          3.170
  Check model and map are aligned:         0.150
  Convert atoms to be neutral:             0.080
  Process input model:                     28.030
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
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      :  0.009   0.128   9769  Z= 0.587
  Angle     :  1.284  17.306  13201  Z= 0.672
  Chirality :  0.065   0.457   1498
  Planarity :  0.007   0.075   1692
  Dihedral  : 13.018  78.710   3556
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.09 %
    Favored  : 88.83 %
  Rotamer Outliers :  1.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -6.63 (0.14), residues: 1226
  helix: -4.93 (0.08), residues: 624
  sheet: -3.53 (0.79), residues: 31
  loop : -3.75 (0.19), residues: 571

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 276
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 3
  residues processed: 284
  average time/residue: 0.2630
  time to fit residues: 99.3095
Evaluate side-chains
  157 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 1.071 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0852
  time to fit residues: 1.9987
-------------------------------------------------------------------------------
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:   20.0000
   chunk 93 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
U  72 HIS
U 170 GLN
U 216 GLN
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 563 GLN
U 598 GLN
U 813 GLN
U 852 ASN
U1097 ASN
U1107 GLN
U1142 HIS
U1194 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9769  Z= 0.231
  Angle     :  0.736  11.630  13201  Z= 0.379
  Chirality :  0.044   0.214   1498
  Planarity :  0.006   0.107   1692
  Dihedral  :  6.775  34.705   1325
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer Outliers :  3.70 %
  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: -5.64 (0.18), residues: 1226
  helix: -4.17 (0.12), residues: 644
  sheet: -2.77 (0.78), residues: 32
  loop : -3.12 (0.23), residues: 550

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 187
  time to evaluate  : 1.188 
Fit side-chains
  outliers start: 38
  outliers final: 15
  residues processed: 211
  average time/residue: 0.2051
  time to fit residues: 61.6046
Evaluate side-chains
  159 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 1.073 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0953
  time to fit residues: 4.1655
-------------------------------------------------------------------------------
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:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0020
   chunk 120 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 110 optimal weight:    0.0470
   chunk 38 optimal weight:    0.3980
   chunk 89 optimal weight:    0.0970
   overall best weight:    0.2684

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

Flipped N/Q/H residues before XYZ refinement:
** U  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 539 ASN
U 563 GLN
U1150 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9769  Z= 0.163
  Angle     :  0.676  11.854  13201  Z= 0.345
  Chirality :  0.042   0.181   1498
  Planarity :  0.006   0.119   1692
  Dihedral  :  5.853  30.412   1325
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer Outliers :  2.92 %
  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 (0.19), residues: 1226
  helix: -3.56 (0.15), residues: 631
  sheet: -2.64 (0.86), residues: 32
  loop : -2.75 (0.23), residues: 563

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 176
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 6
  residues processed: 196
  average time/residue: 0.1954
  time to fit residues: 55.7929
Evaluate side-chains
  150 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 1.063 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0973
  time to fit residues: 2.6588
-------------------------------------------------------------------------------
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:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 118 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0170
   chunk 99 optimal weight:    9.9990
   overall best weight:    3.2024

-------------------------------------------------------------------------------
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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** 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: 0.7307
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9769  Z= 0.377
  Angle     :  0.777  11.771  13201  Z= 0.398
  Chirality :  0.049   0.208   1498
  Planarity :  0.007   0.120   1692
  Dihedral  :  6.250  30.320   1325
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.38 %
    Favored  : 90.54 %
  Rotamer Outliers :  3.80 %
  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: -4.85 (0.20), residues: 1226
  helix: -3.44 (0.15), residues: 654
  sheet: -2.53 (0.74), residues: 37
  loop : -2.82 (0.24), residues: 535

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
  outliers start: 39
  outliers final: 21
  residues processed: 187
  average time/residue: 0.2066
  time to fit residues: 56.0291
Evaluate side-chains
  163 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 1.178 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1093
  time to fit residues: 5.4535
-------------------------------------------------------------------------------
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:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 60 optimal weight:   20.0000
   chunk 106 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 133 ASN
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 563 GLN
U 989 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.113   9769  Z= 0.205
  Angle     :  0.623  10.286  13201  Z= 0.323
  Chirality :  0.044   0.218   1498
  Planarity :  0.006   0.097   1692
  Dihedral  :  5.585  26.142   1325
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer Outliers :  1.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.36 (0.21), residues: 1226
  helix: -3.02 (0.17), residues: 646
  sheet: -1.86 (0.92), residues: 32
  loop : -2.68 (0.24), residues: 548

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 6
  residues processed: 165
  average time/residue: 0.2151
  time to fit residues: 50.3298
Evaluate side-chains
  142 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 1.152 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1062
  time to fit residues: 2.6919
-------------------------------------------------------------------------------
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:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 119 optimal weight:   20.0000
   chunk 98 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0970
   chunk 62 optimal weight:    1.9990
   chunk 114 optimal weight:    9.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 122 ASN
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.151   9769  Z= 0.244
  Angle     :  0.682  18.801  13201  Z= 0.354
  Chirality :  0.044   0.250   1498
  Planarity :  0.006   0.118   1692
  Dihedral  :  5.260  23.876   1325
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer Outliers :  2.43 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.10 (0.21), residues: 1226
  helix: -2.78 (0.18), residues: 649
  sheet: -2.17 (0.81), residues: 38
  loop : -2.55 (0.25), residues: 539

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
  outliers start: 25
  outliers final: 9
  residues processed: 161
  average time/residue: 0.2048
  time to fit residues: 47.7871
Evaluate side-chains
  140 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 1.133 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0997
  time to fit residues: 3.1966
-------------------------------------------------------------------------------
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:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** U  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.112   9769  Z= 0.256
  Angle     :  0.638  11.662  13201  Z= 0.337
  Chirality :  0.044   0.254   1498
  Planarity :  0.007   0.133   1692
  Dihedral  :  5.228  22.345   1325
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer Outliers :  1.75 %
  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: -3.89 (0.22), residues: 1226
  helix: -2.59 (0.18), residues: 651
  sheet: -1.85 (0.82), residues: 38
  loop : -2.50 (0.25), residues: 537

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 8
  residues processed: 152
  average time/residue: 0.1993
  time to fit residues: 44.1778
Evaluate side-chains
  139 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.965 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1023
  time to fit residues: 3.0305
-------------------------------------------------------------------------------
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:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0370
   overall best weight:    1.3464

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

Flipped N/Q/H residues before XYZ refinement:
** U  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 598 GLN
U1161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.5419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.408   9769  Z= 0.411
  Angle     :  0.742  26.189  13201  Z= 0.393
  Chirality :  0.045   0.270   1498
  Planarity :  0.006   0.129   1692
  Dihedral  :  5.150  21.339   1325
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer Outliers :  0.97 %
  Cbeta Deviations :  0.09 %
  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: -3.74 (0.22), residues: 1226
  helix: -2.44 (0.19), residues: 657
  sheet: -1.79 (0.82), residues: 39
  loop : -2.46 (0.25), residues: 530

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 4
  residues processed: 152
  average time/residue: 0.2125
  time to fit residues: 46.4765
Evaluate side-chains
  140 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 1.082 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1144
  time to fit residues: 2.5646
-------------------------------------------------------------------------------
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:    0.1980
   chunk 110 optimal weight:    0.0050
   chunk 113 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    0.1980
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 116 optimal weight:   20.0000
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
** U  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 842 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.5586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.127   9769  Z= 0.229
  Angle     :  0.669  17.441  13201  Z= 0.342
  Chirality :  0.044   0.249   1498
  Planarity :  0.006   0.129   1692
  Dihedral  :  4.973  20.745   1325
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer Outliers :  0.78 %
  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: -3.55 (0.22), residues: 1226
  helix: -2.22 (0.19), residues: 664
  sheet: -1.41 (0.86), residues: 38
  loop : -2.47 (0.25), residues: 524

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 147
  average time/residue: 0.2015
  time to fit residues: 43.1158
Evaluate side-chains
  136 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 1.084 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0911
  time to fit residues: 2.3766
-------------------------------------------------------------------------------
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:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0470
   chunk 10 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 103 optimal weight:   20.0000
   overall best weight:    1.7884

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

Flipped N/Q/H residues before XYZ refinement:
** U  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 598 GLN
U 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.013   0.862   9769  Z= 0.979
  Angle     :  0.915  30.764  13201  Z= 0.502
  Chirality :  0.047   0.245   1498
  Planarity :  0.008   0.177   1692
  Dihedral  :  5.202  21.575   1325
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer Outliers :  0.49 %
  Cbeta Deviations :  0.09 %
  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: -3.46 (0.22), residues: 1226
  helix: -2.19 (0.19), residues: 649
  sheet: -1.15 (0.89), residues: 37
  loop : -2.40 (0.25), residues: 540

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 133
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 137
  average time/residue: 0.1964
  time to fit residues: 39.1134
Evaluate side-chains
  131 residues out of total 1027 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 1.050 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1064
  time to fit residues: 2.4434
-------------------------------------------------------------------------------
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:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0470
   chunk 97 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
** U  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 565 GLN
U 598 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.183608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.138050 restraints weight = 13412.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.137583 restraints weight = 8988.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.138518 restraints weight = 6959.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.5773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.231   9769  Z= 0.350
  Angle     :  0.749  22.937  13201  Z= 0.409
  Chirality :  0.045   0.237   1498
  Planarity :  0.007   0.141   1692
  Dihedral  :  5.075  21.331   1325
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.09 %
  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: -3.47 (0.22), residues: 1226
  helix: -2.10 (0.19), residues: 677
  sheet: -0.96 (0.90), residues: 37
  loop : -2.57 (0.25), residues: 512

===============================================================================
Job complete
usr+sys time: 1941.08 seconds
wall clock time: 36 minutes 4.75 seconds (2164.75 seconds total)