Starting phenix.real_space_refine (version: 1.21rc1)
on Fri Apr 21 08:08:07 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/04_2023/7e1a_30938_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/04_2023/7e1a_30938.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/04_2023/7e1a_30938.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/04_2023/7e1a_30938.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/04_2023/7e1a_30938_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/04_2023/7e1a_30938_updated.pdb"
  }
  resolution = 3.66
  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=   0.006 sd=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5951      2.51       5
     N    1566      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "U ARG  184": "NH1" <-> "NH2"
    Residue "U ARG  303": "NH1" <-> "NH2"
    Residue "U ARG  313": "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  792": "NH1" <-> "NH2"
    Residue "U ARG  832": "NH1" <-> "NH2"
    Residue "U ARG  837": "NH1" <-> "NH2"
    Residue "U ARG  860": "NH1" <-> "NH2"
    Residue "U ARG  920": "NH1" <-> "NH2"
    Residue "U ARG  958": "NH1" <-> "NH2"
    Residue "U ARG 1001": "NH1" <-> "NH2"
    Residue "U ARG 1019": "NH1" <-> "NH2"
    Residue "U ARG 1033": "NH1" <-> "NH2"
    Residue "U ARG 1187": "NH1" <-> "NH2"
    Residue "U ARG 1221": "NH1" <-> "NH2"
    Residue "U ARG 1235": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 9284
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "U"
      Number of atoms: 9284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1190, 9284
          Unusual residues: {'TCH': 1}
          Classifications: {'peptide': 1189, 'undetermined': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 1156, None: 1}
            Not linked:
              pdbres="THR U1315 "
              pdbres="TCH U1401 "
          Chain breaks: 1
  Time building chain proxies: 5.53, per 1000 atoms: 0.60
  Number of scatterers: 9284
  At special positions: 0
  Unit cell: (93.28, 94.34, 161.12, 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    1712      8.00
     N    1566      7.00
     C    5951      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.79
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2190

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      60 helices and 3 sheets defined
      39.7% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'U' and resid 64 through 76
      removed outlier: 3.778A  pdb=" N   CYS U  68 " --> pdb=" O   VAL U  64 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ALA U  69 " --> pdb=" O   GLY U  65 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE U  70 " --> pdb=" O   SER U  66 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   HIS U  72 " --> pdb=" O   CYS U  68 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   ALA U  75 " --> pdb=" O   LEU U  71 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLN U  76 " --> pdb=" O   HIS U  72 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 80 through 83
      No H-bonds generated for 'chain 'U' and resid 80 through 83'
    Processing helix  chain 'U' and resid 89 through 99
      removed outlier: 3.506A  pdb=" N   TYR U  93 " --> pdb=" O   VAL U  89 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 135 through 138
      No H-bonds generated for 'chain 'U' and resid 135 through 138'
    Processing helix  chain 'U' and resid 164 through 167
      No H-bonds generated for 'chain 'U' and resid 164 through 167'
    Processing helix  chain 'U' and resid 171 through 180
      removed outlier: 3.544A  pdb=" N   PHE U 179 " --> pdb=" O   ARG U 175 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 187 through 190
      No H-bonds generated for 'chain 'U' and resid 187 through 190'
    Processing helix  chain 'U' and resid 195 through 198
      No H-bonds generated for 'chain 'U' and resid 195 through 198'
    Processing helix  chain 'U' and resid 228 through 235
      removed outlier: 3.805A  pdb=" N   LEU U 232 " --> pdb=" O   ILE U 228 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU U 233 " --> pdb=" O   CYS U 229 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLY U 234 " --> pdb=" O   GLY U 230 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 246 through 253
      Proline residue:  U 250  - end of helix
    Processing helix  chain 'U' and resid 257 through 263
      removed outlier: 4.042A  pdb=" N   SER U 262 " --> pdb=" O   THR U 258 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL U 263 " --> pdb=" O   ILE U 259 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 268 through 271
      No H-bonds generated for 'chain 'U' and resid 268 through 271'
    Processing helix  chain 'U' and resid 277 through 284
      removed outlier: 4.035A  pdb=" N   ASP U 282 " --> pdb=" O   GLY U 278 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL U 284 " --> pdb=" O   VAL U 280 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 288 through 294
      removed outlier: 3.609A  pdb=" N   PHE U 294 " --> pdb=" O   THR U 290 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 302 through 312
      removed outlier: 3.748A  pdb=" N   LYS U 306 " --> pdb=" O   GLU U 302 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN U 307 " --> pdb=" O   ARG U 303 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LEU U 308 " --> pdb=" O   TYR U 304 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   VAL U 309 " --> pdb=" O   GLU U 305 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   PHE U 310 " --> pdb=" O   LYS U 306 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   ALA U 311 " --> pdb=" O   ASN U 307 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 316 through 323
      removed outlier: 3.669A  pdb=" N   VAL U 321 " --> pdb=" O   ARG U 317 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 332 through 350
      removed outlier: 3.655A  pdb=" N   TYR U 343 " --> pdb=" O   LEU U 339 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU U 347 " --> pdb=" O   TYR U 343 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU U 349 " --> pdb=" O   SER U 345 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 367 through 374
      removed outlier: 4.175A  pdb=" N   ASN U 372 " --> pdb=" O   VAL U 368 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU U 373 " --> pdb=" O   GLY U 369 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY U 374 " --> pdb=" O   ALA U 370 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 381 through 388
      removed outlier: 4.130A  pdb=" N   GLY U 386 " --> pdb=" O   ALA U 382 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 393 through 396
      No H-bonds generated for 'chain 'U' and resid 393 through 396'
    Processing helix  chain 'U' and resid 463 through 466
      No H-bonds generated for 'chain 'U' and resid 463 through 466'
    Processing helix  chain 'U' and resid 491 through 497
      removed outlier: 4.568A  pdb=" N   ASP U 496 " --> pdb=" O   GLN U 492 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN U 497 " --> pdb=" O   TRP U 493 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 512 through 518
      removed outlier: 3.635A  pdb=" N   ILE U 516 " --> pdb=" O   ILE U 512 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG U 517 " --> pdb=" O   ALA U 513 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR U 518 " --> pdb=" O   GLU U 514 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 512 through 518'
    Processing helix  chain 'U' and resid 525 through 534
      removed outlier: 4.588A  pdb=" N   GLN U 530 " --> pdb=" O   GLU U 526 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ALA U 531 " --> pdb=" O   ASP U 527 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA U 532 " --> pdb=" O   ILE U 528 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 539 through 542
      No H-bonds generated for 'chain 'U' and resid 539 through 542'
    Processing helix  chain 'U' and resid 551 through 553
      No H-bonds generated for 'chain 'U' and resid 551 through 553'
    Processing helix  chain 'U' and resid 561 through 573
      removed outlier: 4.503A  pdb=" N   GLN U 565 " --> pdb=" O   GLY U 561 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   ARG U 566 " --> pdb=" O   GLY U 562 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL U 567 " --> pdb=" O   GLN U 563 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA U 570 " --> pdb=" O   ARG U 566 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 591 through 601
      removed outlier: 3.980A  pdb=" N   ALA U 595 " --> pdb=" O   ASN U 591 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET U 596 " --> pdb=" O   GLU U 592 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 651 through 657
      removed outlier: 3.518A  pdb=" N   THR U 655 " --> pdb=" O   PHE U 651 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   LEU U 656 " --> pdb=" O   THR U 652 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 742 through 747
    Processing helix  chain 'U' and resid 749 through 751
      No H-bonds generated for 'chain 'U' and resid 749 through 751'
    Processing helix  chain 'U' and resid 757 through 763
      removed outlier: 3.730A  pdb=" N   GLY U 761 " --> pdb=" O   VAL U 757 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA U 762 " --> pdb=" O   GLY U 758 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 769 through 779
      removed outlier: 3.692A  pdb=" N   PHE U 774 " --> pdb=" O   PRO U 770 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 788 through 822
      removed outlier: 3.956A  pdb=" N   ARG U 792 " --> pdb=" O   LYS U 788 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN U 796 " --> pdb=" O   ARG U 792 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU U 800 " --> pdb=" O   ASN U 796 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU U 801 " --> pdb=" O   GLY U 797 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE U 802 " --> pdb=" O   VAL U 798 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   VAL U 803 " --> pdb=" O   CYS U 799 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA U 804 " --> pdb=" O   LEU U 800 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER U 809 " --> pdb=" O   MET U 805 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU U 810 " --> pdb=" O   GLY U 806 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE U 811 " --> pdb=" O   CYS U 807 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLN U 813 " --> pdb=" O   SER U 809 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU U 815 " --> pdb=" O   PHE U 811 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLN U 816 " --> pdb=" O   THR U 812 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY U 817 " --> pdb=" O   GLN U 813 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA U 819 " --> pdb=" O   LEU U 815 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   PHE U 820 " --> pdb=" O   GLN U 816 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ALA U 821 " --> pdb=" O   GLY U 817 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 830 through 838
    Processing helix  chain 'U' and resid 844 through 846
      No H-bonds generated for 'chain 'U' and resid 844 through 846'
    Processing helix  chain 'U' and resid 856 through 863
      removed outlier: 4.971A  pdb=" N   LEU U 861 " --> pdb=" O   LEU U 857 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA U 862 " --> pdb=" O   THR U 858 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR U 863 " --> pdb=" O   THR U 859 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 873 through 876
      No H-bonds generated for 'chain 'U' and resid 873 through 876'
    Processing helix  chain 'U' and resid 881 through 887
      removed outlier: 4.628A  pdb=" N   VAL U 886 " --> pdb=" O   SER U 882 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 889 through 895
    Processing helix  chain 'U' and resid 901 through 912
      removed outlier: 3.612A  pdb=" N   LEU U 905 " --> pdb=" O   SER U 901 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE U 907 " --> pdb=" O   VAL U 903 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE U 908 " --> pdb=" O   ILE U 904 " (cutoff:3.500A)
      Proline residue:  U 909  - end of helix
      removed outlier: 3.529A  pdb=" N   ALA U 912 " --> pdb=" O   PHE U 908 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 919 through 922
      No H-bonds generated for 'chain 'U' and resid 919 through 922'
    Processing helix  chain 'U' and resid 930 through 933
      No H-bonds generated for 'chain 'U' and resid 930 through 933'
    Processing helix  chain 'U' and resid 936 through 939
      No H-bonds generated for 'chain 'U' and resid 936 through 939'
    Processing helix  chain 'U' and resid 947 through 950
      No H-bonds generated for 'chain 'U' and resid 947 through 950'
    Processing helix  chain 'U' and resid 957 through 967
      removed outlier: 4.539A  pdb=" N   LEU U 963 " --> pdb=" O   PHE U 959 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU U 964 " --> pdb=" O   ILE U 960 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR U 965 " --> pdb=" O   GLU U 961 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   GLU U 966 " --> pdb=" O   ALA U 962 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 995 through 1009
      removed outlier: 3.659A  pdb=" N   SER U 999 " --> pdb=" O   ALA U 995 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR U1000 " --> pdb=" O   ASN U 996 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR U1002 " --> pdb=" O   ALA U 998 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER U1008 " --> pdb=" O   GLY U1004 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASN U1009 " --> pdb=" O   TYR U1005 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1014 through 1021
      removed outlier: 3.736A  pdb=" N   PHE U1018 " --> pdb=" O   SER U1015 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ARG U1019 " --> pdb=" O   TYR U1016 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL U1020 " --> pdb=" O   VAL U1017 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ILE U1021 " --> pdb=" O   PHE U1018 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1026 through 1035
      removed outlier: 3.622A  pdb=" N   ALA U1030 " --> pdb=" O   LEU U1026 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU U1031 " --> pdb=" O   SER U1027 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA U1034 " --> pdb=" O   ALA U1030 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1041 through 1055
      removed outlier: 4.102A  pdb=" N   LYS U1045 " --> pdb=" O   ALA U1042 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ILE U1046 " --> pdb=" O   LYS U1043 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA U1048 " --> pdb=" O   LYS U1045 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ALA U1049 " --> pdb=" O   ILE U1046 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ARG U1050 " --> pdb=" O   SER U1047 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE U1052 " --> pdb=" O   ALA U1049 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   GLN U1053 " --> pdb=" O   ARG U1050 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1121 through 1124
      No H-bonds generated for 'chain 'U' and resid 1121 through 1124'
    Processing helix  chain 'U' and resid 1144 through 1146
      No H-bonds generated for 'chain 'U' and resid 1144 through 1146'
    Processing helix  chain 'U' and resid 1149 through 1152
      No H-bonds generated for 'chain 'U' and resid 1149 through 1152'
    Processing helix  chain 'U' and resid 1170 through 1177
      removed outlier: 3.564A  pdb=" N   ILE U1174 " --> pdb=" O   ILE U1170 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1186 through 1194
      removed outlier: 4.083A  pdb=" N   ALA U1190 " --> pdb=" O   GLU U1186 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA U1192 " --> pdb=" O   VAL U1188 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS U1193 " --> pdb=" O   ILE U1189 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1200 through 1203
      No H-bonds generated for 'chain 'U' and resid 1200 through 1203'
    Processing helix  chain 'U' and resid 1221 through 1234
      removed outlier: 4.231A  pdb=" N   ARG U1226 " --> pdb=" O   GLY U1222 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ILE U1227 " --> pdb=" O   GLU U1223 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA U1228 " --> pdb=" O   LYS U1224 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA U1230 " --> pdb=" O   ARG U1226 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA U1232 " --> pdb=" O   ALA U1228 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL U1234 " --> pdb=" O   ALA U1230 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1253 through 1263
      removed outlier: 3.559A  pdb=" N   GLN U1258 " --> pdb=" O   GLU U1254 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL U1259 " --> pdb=" O   LYS U1255 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA U1260 " --> pdb=" O   THR U1256 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1300 through 1302
      No H-bonds generated for 'chain 'U' and resid 1300 through 1302'
    Processing helix  chain 'U' and resid 1309 through 1313
    Processing sheet with id=  A, first strand: chain 'U' and resid 420 through 422
    Processing sheet with id=  B, first strand: chain 'U' and resid 498 through 501
      removed outlier: 6.406A  pdb=" N   ILE U 579 " --> pdb=" O   GLY U 499 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   VAL U 501 " --> pdb=" O   ILE U 579 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LEU U 581 " --> pdb=" O   VAL U 501 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   THR U 609 " --> pdb=" O   LEU U 580 " (cutoff:3.500A)
      removed outlier: 8.456A  pdb=" N   LEU U 582 " --> pdb=" O   THR U 609 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ILE U 611 " --> pdb=" O   LEU U 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'U' and resid 1156 through 1159
      removed outlier: 6.338A  pdb=" N   ILE U1239 " --> pdb=" O   GLY U1157 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   VAL U1159 " --> pdb=" O   ILE U1239 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU U1241 " --> pdb=" O   VAL U1159 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C

    127 hydrogen bonds defined for protein.
    357 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: 2.43

  Time building geometry restraints manager: 4.11 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: 2349
        1.33 -     1.45: 1944
        1.45 -     1.57: 5082
        1.57 -     1.69: 1
        1.69 -     1.81: 89
  Bond restraints: 9465
  Sorted by residual:
  bond pdb=" C   ALA U 214 "
       pdb=" N   ASP U 215 "
    ideal  model  delta    sigma   weight residual
    1.335  1.269  0.065 1.42e-02 4.96e+03 2.12e+01
  bond pdb=" O3S TCH U1401 "
       pdb=" S26 TCH U1401 "
    ideal  model  delta    sigma   weight residual
    1.475  1.549 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" CG1 ILE U 171 "
       pdb=" CD1 ILE U 171 "
    ideal  model  delta    sigma   weight residual
    1.513  1.376  0.137 3.90e-02 6.57e+02 1.23e+01
  bond pdb=" CG1 ILE U 245 "
       pdb=" CD1 ILE U 245 "
    ideal  model  delta    sigma   weight residual
    1.513  1.382  0.131 3.90e-02 6.57e+02 1.13e+01
  bond pdb=" CB  VAL U1024 "
       pdb=" CG2 VAL U1024 "
    ideal  model  delta    sigma   weight residual
    1.521  1.419  0.102 3.30e-02 9.18e+02 9.62e+00
  ... (remaining 9460 not shown)

  Histogram of bond angle deviations from ideal:
       96.30 -   106.24: 222
      106.24 -   116.17: 5873
      116.17 -   126.11: 6594
      126.11 -   136.04: 116
      136.04 -   145.98: 1
  Bond angle restraints: 12806
  Sorted by residual:
  angle pdb=" N   VAL U 152 "
        pdb=" CA  VAL U 152 "
        pdb=" C   VAL U 152 "
      ideal   model   delta    sigma   weight residual
     113.20  104.66    8.54 9.60e-01 1.09e+00 7.91e+01
  angle pdb=" C   HIS U1013 "
        pdb=" N   PHE U1014 "
        pdb=" CA  PHE U1014 "
      ideal   model   delta    sigma   weight residual
     120.82  131.96  -11.14 1.50e+00 4.44e-01 5.52e+01
  angle pdb=" N   ILE U 158 "
        pdb=" CA  ILE U 158 "
        pdb=" C   ILE U 158 "
      ideal   model   delta    sigma   weight residual
     113.53  106.72    6.81 9.80e-01 1.04e+00 4.83e+01
  angle pdb=" N   ILE U 221 "
        pdb=" CA  ILE U 221 "
        pdb=" C   ILE U 221 "
      ideal   model   delta    sigma   weight residual
     111.91  105.90    6.01 8.90e-01 1.26e+00 4.56e+01
  angle pdb=" N   VAL U1017 "
        pdb=" CA  VAL U1017 "
        pdb=" C   VAL U1017 "
      ideal   model   delta    sigma   weight residual
     112.96  106.66    6.30 1.00e+00 1.00e+00 3.97e+01
  ... (remaining 12801 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 5021
       15.42 -    30.84: 467
       30.84 -    46.25: 112
       46.25 -    61.67: 4
       61.67 -    77.09: 13
  Dihedral angle restraints: 5617
    sinusoidal: 2206
      harmonic: 3411
  Sorted by residual:
  dihedral pdb=" CA  PRO U1039 "
           pdb=" C   PRO U1039 "
           pdb=" N   SER U1040 "
           pdb=" CA  SER U1040 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.85  -31.15     0      5.00e+00 4.00e-02 3.88e+01
  dihedral pdb=" CA  ARG U 181 "
           pdb=" C   ARG U 181 "
           pdb=" N   ILE U 182 "
           pdb=" CA  ILE U 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.73   30.27     0      5.00e+00 4.00e-02 3.67e+01
  dihedral pdb=" CA  ILE U 362 "
           pdb=" C   ILE U 362 "
           pdb=" N   PHE U 363 "
           pdb=" CA  PHE U 363 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.24   29.76     0      5.00e+00 4.00e-02 3.54e+01
  ... (remaining 5614 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 989
       0.063 -    0.126: 380
       0.126 -    0.189: 66
       0.189 -    0.251: 20
       0.251 -    0.314: 7
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CB  VAL U 764 "
            pdb=" CA  VAL U 764 "
            pdb=" CG1 VAL U 764 "
            pdb=" CG2 VAL U 764 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  ILE U 221 "
            pdb=" CA  ILE U 221 "
            pdb=" CG1 ILE U 221 "
            pdb=" CG2 ILE U 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  VAL U 248 "
            pdb=" CA  VAL U 248 "
            pdb=" CG1 VAL U 248 "
            pdb=" CG2 VAL U 248 "
    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 1459 not shown)

  Planarity restraints: 1631
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 TCH U1401 "    0.142 2.00e-02 2.50e+03   1.65e-01 3.39e+02
        pdb=" C24 TCH U1401 "   -0.054 2.00e-02 2.50e+03
        pdb=" C25 TCH U1401 "    0.198 2.00e-02 2.50e+03
        pdb=" N24 TCH U1401 "   -0.270 2.00e-02 2.50e+03
        pdb=" O24 TCH U1401 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS U 969 "    0.051 5.00e-02 4.00e+02   7.57e-02 9.16e+00
        pdb=" N   PRO U 970 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO U 970 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO U 970 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN U  76 "    0.050 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO U  77 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO U  77 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO U  77 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1628 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2071
        2.77 -     3.30: 8590
        3.30 -     3.83: 14597
        3.83 -     4.37: 17075
        4.37 -     4.90: 28378
  Nonbonded interactions: 70711
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP U 864 "
            pdb=" OG  SER U1047 "
     model   vdw
     2.233 2.440
  nonbonded pdb=" O   SER U 809 "
            pdb=" OG  SER U 809 "
     model   vdw
     2.238 2.440
  nonbonded pdb=" OH  TYR U 145 "
            pdb=" O2S TCH U1401 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" OG1 THR U 355 "
            pdb=" OG1 THR U 358 "
     model   vdw
     2.260 2.440
  nonbonded pdb=" O   THR U 155 "
            pdb=" OG1 THR U 155 "
     model   vdw
     2.262 2.440
  ... (remaining 70706 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.290
  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:             0.000
  Extract box with map and model:          2.910
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     27.620
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
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      :  0.012   0.137   9465  Z= 0.796
  Angle     :  1.391  25.169  12806  Z= 0.775
  Chirality :  0.069   0.314   1462
  Planarity :  0.009   0.165   1631
  Dihedral  : 13.288  77.090   3427
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.65 %
    Favored  : 88.27 %
  Rotamer Outliers :  0.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -6.43 (0.15), residues: 1185
  helix: -4.74 (0.08), residues: 637
  sheet: -4.05 (0.64), residues: 37
  loop : -3.46 (0.22), residues: 511

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 209
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 1
  residues processed: 216
  average time/residue: 0.2834
  time to fit residues: 81.1222
Evaluate side-chains
  119 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.994 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0798
  time to fit residues: 1.5689
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0060
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 503 GLN
U 515 ASN
U 598 GLN
U 605 GLN
U 640 HIS
U 842 GLN
U 931 GLN
U1196 GLN
** U1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9465  Z= 0.180
  Angle     :  0.703  19.404  12806  Z= 0.355
  Chirality :  0.042   0.160   1462
  Planarity :  0.005   0.044   1631
  Dihedral  :  7.576  92.223   1288
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer Outliers :  2.83 %
  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: -5.65 (0.18), residues: 1185
  helix: -4.05 (0.12), residues: 641
  sheet: -3.76 (0.75), residues: 40
  loop : -3.14 (0.23), residues: 504

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 8
  residues processed: 169
  average time/residue: 0.2154
  time to fit residues: 51.1240
Evaluate side-chains
  124 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 1.093 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 8
  outliers final: 1
  residues processed: 8
  average time/residue: 0.0963
  time to fit residues: 2.9072
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0470
   chunk 96 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.8880

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 546 GLN
U1134 GLN
U1258 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9465  Z= 0.174
  Angle     :  0.653  20.341  12806  Z= 0.318
  Chirality :  0.041   0.202   1462
  Planarity :  0.004   0.034   1631
  Dihedral  :  6.730  87.779   1288
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer Outliers :  2.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.11 (0.19), residues: 1185
  helix: -3.49 (0.15), residues: 651
  sheet: -2.77 (1.11), residues: 25
  loop : -3.14 (0.24), residues: 509

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 9
  residues processed: 149
  average time/residue: 0.2046
  time to fit residues: 43.9490
Evaluate side-chains
  116 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 1.124 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 9
  outliers final: 1
  residues processed: 9
  average time/residue: 0.1019
  time to fit residues: 3.2478
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.0060
   chunk 81 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 108 optimal weight:    7.9990
   chunk 115 optimal weight:   20.0000
   chunk 102 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.9002

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 546 GLN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9465  Z= 0.270
  Angle     :  0.686  19.445  12806  Z= 0.335
  Chirality :  0.044   0.211   1462
  Planarity :  0.004   0.032   1631
  Dihedral  :  6.728  86.104   1288
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer Outliers :  3.04 %
  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: -4.66 (0.21), residues: 1185
  helix: -3.19 (0.16), residues: 640
  sheet: -2.61 (1.15), residues: 25
  loop : -2.84 (0.25), residues: 520

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1935
  time to fit residues: 39.4318
Evaluate side-chains
  122 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 1.150 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 16
  outliers final: 1
  residues processed: 16
  average time/residue: 0.0968
  time to fit residues: 4.4423
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 85 optimal weight:    0.6980
   chunk 47 optimal weight:    7.9990
   chunk 98 optimal weight:   20.0000
   chunk 79 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 515 ASN
** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 842 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9465  Z= 0.330
  Angle     :  0.706  18.403  12806  Z= 0.345
  Chirality :  0.045   0.235   1462
  Planarity :  0.004   0.035   1631
  Dihedral  :  6.795  88.451   1288
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer Outliers :  2.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.48 (0.21), residues: 1185
  helix: -3.06 (0.17), residues: 635
  sheet: -2.65 (1.18), residues: 25
  loop : -2.73 (0.25), residues: 525

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1923
  time to fit residues: 35.7688
Evaluate side-chains
  115 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 1.100 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 10
  outliers final: 1
  residues processed: 10
  average time/residue: 0.0987
  time to fit residues: 3.1891
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 115 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 605 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9465  Z= 0.267
  Angle     :  0.667  17.881  12806  Z= 0.323
  Chirality :  0.043   0.201   1462
  Planarity :  0.003   0.032   1631
  Dihedral  :  6.617  91.302   1288
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer Outliers :  1.72 %
  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: -4.26 (0.22), residues: 1185
  helix: -2.87 (0.18), residues: 633
  sheet: -2.50 (1.19), residues: 25
  loop : -2.66 (0.25), residues: 527

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 8
  residues processed: 117
  average time/residue: 0.2058
  time to fit residues: 35.1553
Evaluate side-chains
  107 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 1.110 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0985
  time to fit residues: 2.9561
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 96 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 114 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 423 HIS
** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9465  Z= 0.270
  Angle     :  0.662  17.640  12806  Z= 0.321
  Chirality :  0.043   0.232   1462
  Planarity :  0.003   0.033   1631
  Dihedral  :  6.550  91.519   1288
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer Outliers :  1.92 %
  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: -4.16 (0.22), residues: 1185
  helix: -2.77 (0.18), residues: 631
  sheet: -2.35 (1.24), residues: 25
  loop : -2.64 (0.26), residues: 529

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 6
  residues processed: 119
  average time/residue: 0.1971
  time to fit residues: 34.7498
Evaluate side-chains
  105 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 1.086 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0988
  time to fit residues: 2.6395
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 72 optimal weight:    0.0770
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0980
   chunk 10 optimal weight:    0.0040
   chunk 90 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.3550

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 546 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9465  Z= 0.130
  Angle     :  0.627  18.293  12806  Z= 0.295
  Chirality :  0.040   0.247   1462
  Planarity :  0.003   0.031   1631
  Dihedral  :  5.948  92.804   1288
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer Outliers :  1.01 %
  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: -3.77 (0.23), residues: 1185
  helix: -2.43 (0.19), residues: 637
  sheet: -2.18 (1.21), residues: 25
  loop : -2.50 (0.26), residues: 523

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 1.130 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 119
  average time/residue: 0.2149
  time to fit residues: 37.3718
Evaluate side-chains
  103 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 1.102 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1753
  time to fit residues: 2.5489
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0770
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 101 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9980
   chunk 113 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0370
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 791 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9465  Z= 0.140
  Angle     :  0.638  18.083  12806  Z= 0.298
  Chirality :  0.040   0.252   1462
  Planarity :  0.003   0.076   1631
  Dihedral  :  5.721  89.815   1288
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer Outliers :  0.81 %
  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: -3.58 (0.23), residues: 1185
  helix: -2.22 (0.19), residues: 649
  sheet: -2.38 (0.99), residues: 32
  loop : -2.45 (0.27), residues: 504

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2180
  time to fit residues: 36.7917
Evaluate side-chains
  99 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 1.172 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0993
  time to fit residues: 2.6696
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 78 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0010
   chunk 109 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.8592

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

Flipped N/Q/H residues before XYZ refinement:
U 170 GLN
U 546 GLN
U 791 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9465  Z= 0.263
  Angle     :  0.694  16.744  12806  Z= 0.332
  Chirality :  0.044   0.240   1462
  Planarity :  0.004   0.077   1631
  Dihedral  :  6.037  87.689   1288
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer Outliers :  0.51 %
  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: -3.63 (0.23), residues: 1185
  helix: -2.31 (0.19), residues: 640
  sheet: -2.57 (0.90), residues: 38
  loop : -2.38 (0.27), residues: 507

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 105
  average time/residue: 0.2219
  time to fit residues: 33.9548
Evaluate side-chains
  100 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 1.174 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1020
  time to fit residues: 2.1891
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 97 optimal weight:   40.0000
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 68 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 546 GLN
U 791 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.182947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.116529 restraints weight = 13958.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.119960 restraints weight = 7848.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122253 restraints weight = 5448.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9465  Z= 0.160
  Angle     :  0.650  17.085  12806  Z= 0.308
  Chirality :  0.041   0.242   1462
  Planarity :  0.003   0.063   1631
  Dihedral  :  5.759  90.515   1288
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer Outliers :  0.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.23), residues: 1185
  helix: -2.05 (0.19), residues: 642
  sheet: -2.46 (0.92), residues: 38
  loop : -2.31 (0.27), residues: 505

===============================================================================
Job complete
usr+sys time: 1918.02 seconds
wall clock time: 35 minutes 42.73 seconds (2142.73 seconds total)