Starting phenix.real_space_refine
on Fri Dec  8 22:46:21 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/12_2023/7dv5_30870_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/12_2023/7dv5_30870.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/12_2023/7dv5_30870.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/12_2023/7dv5_30870.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/12_2023/7dv5_30870_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/12_2023/7dv5_30870_updated.pdb"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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      56      5.16       5
     C    5977      2.51       5
     N    1567      2.21       5
     O    1719      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  299": "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 PHE  651": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ARG  792": "NH1" <-> "NH2"
    Residue "U ARG  832": "NH1" <-> "NH2"
    Residue "U ARG  860": "NH1" <-> "NH2"
    Residue "U ARG  957": "NH1" <-> "NH2"
    Residue "U ARG  958": "NH1" <-> "NH2"
    Residue "U ARG 1019": "NH1" <-> "NH2"
    Residue "U ARG 1187": "NH1" <-> "NH2"
    Residue "U ARG 1221": "NH1" <-> "NH2"
    Residue "U ARG 1235": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 9319
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "U"
      Number of atoms: 9319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1191, 9319
          Unusual residues: {'TCH': 2}
          Classifications: {'peptide': 1189, 'undetermined': 2}
          Link IDs: {'PTRANS': 32, 'TRANS': 1156, None: 2}
            Not linked:
              pdbres="THR U1315 "
              pdbres="TCH U1401 "
            Not linked:
              pdbres="TCH U1401 "
              pdbres="TCH U1402 "
          Chain breaks: 1
  Time building chain proxies: 5.51, per 1000 atoms: 0.59
  Number of scatterers: 9319
  At special positions: 0
  Unit cell: (91.91, 157.56, 96.96, 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      56     16.00
     O    1719      8.00
     N    1567      7.00
     C    5977      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: 3.33
  Conformation dependent library (CDL) restraints added in 1.9 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:
      59 helices and 3 sheets defined
      37.4% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.80
  Creating SS restraints...
    Processing helix  chain 'U' and resid 56 through 58
      No H-bonds generated for 'chain 'U' and resid 56 through 58'
    Processing helix  chain 'U' and resid 75 through 86
      removed outlier: 4.652A  pdb=" N   LEU U  80 " --> pdb=" O   GLN U  76 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU U  81 " --> pdb=" O   PRO U  77 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE U  82 " --> pdb=" O   GLY U  78 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 89 through 98
      removed outlier: 3.853A  pdb=" N   VAL U  95 " --> pdb=" O   ILE U  91 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLU U  96 " --> pdb=" O   ASP U  92 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 135 through 153
      removed outlier: 3.701A  pdb=" N   ILE U 139 " --> pdb=" O   GLU U 135 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   LYS U 140 " --> pdb=" O   SER U 136 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER U 143 " --> pdb=" O   ILE U 139 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   TYR U 144 " --> pdb=" O   LYS U 140 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA U 146 " --> pdb=" O   ALA U 142 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY U 147 " --> pdb=" O   SER U 143 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL U 150 " --> pdb=" O   ALA U 146 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 158 through 161
      No H-bonds generated for 'chain 'U' and resid 158 through 161'
    Processing helix  chain 'U' and resid 171 through 183
      removed outlier: 3.914A  pdb=" N   LYS U 176 " --> pdb=" O   GLN U 172 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   PHE U 179 " --> pdb=" O   ARG U 175 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   MET U 183 " --> pdb=" O   PHE U 179 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 188 through 192
      removed outlier: 4.124A  pdb=" N   CYS U 192 " --> pdb=" O   GLY U 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 188 through 192'
    Processing helix  chain 'U' and resid 215 through 235
      removed outlier: 3.667A  pdb=" N   LEU U 219 " --> pdb=" O   ASP U 215 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   PHE U 220 " --> pdb=" O   GLN U 216 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ARG U 223 " --> pdb=" O   LEU U 219 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER U 226 " --> pdb=" O   GLN U 222 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   THR U 227 " --> pdb=" O   ARG U 223 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   CYS U 229 " --> pdb=" O   THR U 225 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   PHE U 231 " --> pdb=" O   THR U 227 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLY U 234 " --> pdb=" O   GLY U 230 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 239 through 242
      No H-bonds generated for 'chain 'U' and resid 239 through 242'
    Processing helix  chain 'U' and resid 245 through 249
    Processing helix  chain 'U' and resid 251 through 257
      removed outlier: 3.777A  pdb=" N   GLY U 255 " --> pdb=" O   LEU U 251 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA U 256 " --> pdb=" O   ILE U 252 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 267 through 274
      removed outlier: 3.864A  pdb=" N   LEU U 271 " --> pdb=" O   THR U 267 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 288 through 294
      removed outlier: 3.665A  pdb=" N   ALA U 292 " --> pdb=" O   MET U 288 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA U 293 " --> pdb=" O   ARG U 289 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE U 294 " --> pdb=" O   THR U 290 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 288 through 294'
    Processing helix  chain 'U' and resid 297 through 300
      No H-bonds generated for 'chain 'U' and resid 297 through 300'
    Processing helix  chain 'U' and resid 302 through 305
      No H-bonds generated for 'chain 'U' and resid 302 through 305'
    Processing helix  chain 'U' and resid 321 through 334
      removed outlier: 3.834A  pdb=" N   THR U 326 " --> pdb=" O   MET U 322 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY U 327 " --> pdb=" O   GLY U 323 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU U 332 " --> pdb=" O   PHE U 328 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 343 through 349
      removed outlier: 4.114A  pdb=" N   LEU U 347 " --> pdb=" O   TYR U 343 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL U 348 " --> pdb=" O   GLY U 344 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 363 through 376
      removed outlier: 3.832A  pdb=" N   ASN U 372 " --> pdb=" O   VAL U 368 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU U 373 " --> pdb=" O   GLY U 369 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY U 374 " --> pdb=" O   ALA U 370 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA U 376 " --> pdb=" O   ASN U 372 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 382 through 389
    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 491 through 497
      removed outlier: 3.924A  pdb=" N   ASP U 496 " --> pdb=" O   GLN U 492 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLN U 497 " --> pdb=" O   TRP U 493 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 525 through 534
      removed outlier: 3.962A  pdb=" N   VAL U 529 " --> pdb=" O   MET U 525 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLN U 530 " --> pdb=" O   GLU U 526 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA U 531 " --> pdb=" O   ASP U 527 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU U 534 " --> pdb=" O   GLN U 530 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 538 through 542
    Processing helix  chain 'U' and resid 561 through 573
      removed outlier: 4.177A  pdb=" N   ARG U 566 " --> pdb=" O   GLY U 562 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   VAL U 567 " --> pdb=" O   GLN U 563 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA U 568 " --> pdb=" O   LYS U 564 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE U 569 " --> pdb=" O   GLN U 565 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA U 570 " --> pdb=" O   ARG U 566 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 594 through 602
      removed outlier: 3.682A  pdb=" N   VAL U 600 " --> pdb=" O   MET U 596 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU U 601 " --> pdb=" O   VAL U 597 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 653 through 655
      No H-bonds generated for 'chain 'U' and resid 653 through 655'
    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 754 through 764
      removed outlier: 3.548A  pdb=" N   ALA U 762 " --> pdb=" O   GLY U 758 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ALA U 763 " --> pdb=" O   SER U 759 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL U 764 " --> pdb=" O   VAL U 760 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 768 through 779
      removed outlier: 3.519A  pdb=" N   TYR U 772 " --> pdb=" O   VAL U 768 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ALA U 773 " --> pdb=" O   THR U 769 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE U 774 " --> pdb=" O   PRO U 770 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER U 777 " --> pdb=" O   ALA U 773 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLN U 778 " --> pdb=" O   PHE U 774 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 790 through 793
      No H-bonds generated for 'chain 'U' and resid 790 through 793'
    Processing helix  chain 'U' and resid 803 through 818
      removed outlier: 3.884A  pdb=" N   VAL U 808 " --> pdb=" O   ALA U 804 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   PHE U 811 " --> pdb=" O   CYS U 807 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLN U 813 " --> pdb=" O   SER U 809 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   PHE U 814 " --> pdb=" O   LEU U 810 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 820 through 840
      removed outlier: 3.828A  pdb=" N   GLY U 824 " --> pdb=" O   PHE U 820 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   GLU U 825 " --> pdb=" O   ALA U 821 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR U 828 " --> pdb=" O   GLY U 824 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG U 830 " --> pdb=" O   LEU U 826 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG U 832 " --> pdb=" O   THR U 828 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS U 833 " --> pdb=" O   LYS U 829 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 854 through 857
      No H-bonds generated for 'chain 'U' and resid 854 through 857'
    Processing helix  chain 'U' and resid 868 through 879
      removed outlier: 3.913A  pdb=" N   ALA U 872 " --> pdb=" O   GLN U 869 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   GLY U 873 " --> pdb=" O   GLY U 870 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   SER U 874 " --> pdb=" O   ALA U 871 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLN U 875 " --> pdb=" O   ALA U 872 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ILE U 876 " --> pdb=" O   GLY U 873 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 888 through 896
      removed outlier: 3.910A  pdb=" N   PHE U 896 " --> pdb=" O   ILE U 892 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 901 through 906
      removed outlier: 3.867A  pdb=" N   CYS U 906 " --> pdb=" O   LEU U 902 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 909 through 916
      removed outlier: 3.539A  pdb=" N   LEU U 913 " --> pdb=" O   PRO U 909 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER U 914 " --> pdb=" O   PHE U 910 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 923 through 925
      No H-bonds generated for 'chain 'U' and resid 923 through 925'
    Processing helix  chain 'U' and resid 930 through 932
      No H-bonds generated for 'chain 'U' and resid 930 through 932'
    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 948 through 951
      No H-bonds generated for 'chain 'U' and resid 948 through 951'
    Processing helix  chain 'U' and resid 966 through 972
      removed outlier: 3.526A  pdb=" N   LYS U 969 " --> pdb=" O   GLU U 966 " (cutoff:3.500A)
      Proline residue:  U 970  - end of helix
      No H-bonds generated for 'chain 'U' and resid 966 through 972'
    Processing helix  chain 'U' and resid 981 through 984
      No H-bonds generated for 'chain 'U' and resid 981 through 984'
    Processing helix  chain 'U' and resid 992 through 995
      No H-bonds generated for 'chain 'U' and resid 992 through 995'
    Processing helix  chain 'U' and resid 997 through 1008
      removed outlier: 3.733A  pdb=" N   ARG U1001 " --> pdb=" O   SER U 997 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   TYR U1002 " --> pdb=" O   ALA U 998 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU U1006 " --> pdb=" O   TYR U1002 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER U1008 " --> pdb=" O   GLY U1004 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1015 through 1018
      No H-bonds generated for 'chain 'U' and resid 1015 through 1018'
    Processing helix  chain 'U' and resid 1030 through 1033
      No H-bonds generated for 'chain 'U' and resid 1030 through 1033'
    Processing helix  chain 'U' and resid 1048 through 1055
      removed outlier: 3.596A  pdb=" N   PHE U1052 " --> pdb=" O   ALA U1048 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLN U1053 " --> pdb=" O   ALA U1049 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1120 through 1124
    Processing helix  chain 'U' and resid 1149 through 1153
    Processing helix  chain 'U' and resid 1170 through 1177
      removed outlier: 3.927A  pdb=" N   GLY U1177 " --> pdb=" O   ASN U1173 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1186 through 1190
      removed outlier: 3.844A  pdb=" N   ALA U1190 " --> pdb=" O   GLU U1186 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 1186 through 1190'
    Processing helix  chain 'U' and resid 1221 through 1223
      No H-bonds generated for 'chain 'U' and resid 1221 through 1223'
    Processing helix  chain 'U' and resid 1225 through 1228
      No H-bonds generated for 'chain 'U' and resid 1225 through 1228'
    Processing helix  chain 'U' and resid 1230 through 1233
      No H-bonds generated for 'chain 'U' and resid 1230 through 1233'
    Processing helix  chain 'U' and resid 1251 through 1263
      removed outlier: 3.717A  pdb=" N   THR U1256 " --> pdb=" O   GLU U1252 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA U1260 " --> pdb=" O   THR U1256 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP U1262 " --> pdb=" O   GLN U1258 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS U1263 " --> pdb=" O   VAL U1259 " (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 1314
      removed outlier: 4.061A  pdb=" N   LEU U1313 " --> pdb=" O   ALA U1309 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'U' and resid 420 through 422
      removed outlier: 3.627A  pdb=" N   ILE U 420 " --> pdb=" O   ILE U 445 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET U 443 " --> pdb=" O   PHE U 422 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'U' and resid 498 through 501
      removed outlier: 6.483A  pdb=" N   ILE U 579 " --> pdb=" O   GLY U 499 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   VAL U 501 " --> pdb=" O   ILE U 579 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU U 581 " --> pdb=" O   VAL U 501 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   THR U 609 " --> pdb=" O   LEU U 580 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   LEU U 582 " --> pdb=" O   THR U 609 " (cutoff:3.500A)
      removed outlier: 7.150A  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: 6.586A  pdb=" N   ILE U1239 " --> pdb=" O   GLY U1157 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   VAL U1159 " --> pdb=" O   ILE U1239 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU U1241 " --> pdb=" O   VAL U1159 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C

    125 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: 2.54

  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: 2531
        1.33 -     1.45: 1907
        1.45 -     1.57: 4975
        1.57 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 9503
  Sorted by residual:
  bond pdb=" CG1 ILE U 171 "
       pdb=" CD1 ILE U 171 "
    ideal  model  delta    sigma   weight residual
    1.513  1.365  0.148 3.90e-02 6.57e+02 1.43e+01
  bond pdb=" O3S TCH U1401 "
       pdb=" S26 TCH U1401 "
    ideal  model  delta    sigma   weight residual
    1.475  1.548 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" O3S TCH U1402 "
       pdb=" S26 TCH U1402 "
    ideal  model  delta    sigma   weight residual
    1.475  1.547 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" N   VAL U 348 "
       pdb=" CA  VAL U 348 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.22e-02 6.72e+03 9.19e+00
  bond pdb=" N   ILE U1280 "
       pdb=" CA  ILE U1280 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.25e-02 6.40e+03 8.69e+00
  ... (remaining 9498 not shown)

  Histogram of bond angle deviations from ideal:
       75.84 -    90.96: 2
       90.96 -   106.08: 202
      106.08 -   121.21: 10162
      121.21 -   136.33: 2498
      136.33 -   151.45: 2
  Bond angle restraints: 12866
  Sorted by residual:
  angle pdb=" N   ARG U 920 "
        pdb=" CA  ARG U 920 "
        pdb=" C   ARG U 920 "
      ideal   model   delta    sigma   weight residual
     110.80  151.45  -40.65 2.13e+00 2.20e-01 3.64e+02
  angle pdb=" N   ILE U 112 "
        pdb=" CA  ILE U 112 "
        pdb=" C   ILE U 112 "
      ideal   model   delta    sigma   weight residual
     110.62  132.26  -21.64 1.14e+00 7.69e-01 3.60e+02
  angle pdb=" C   ARG U 920 "
        pdb=" CA  ARG U 920 "
        pdb=" CB  ARG U 920 "
      ideal   model   delta    sigma   weight residual
     110.42   75.84   34.58 1.99e+00 2.53e-01 3.02e+02
  angle pdb=" N   THR U 111 "
        pdb=" CA  THR U 111 "
        pdb=" C   THR U 111 "
      ideal   model   delta    sigma   weight residual
     108.00   82.83   25.17 1.48e+00 4.57e-01 2.89e+02
  angle pdb=" C   THR U 111 "
        pdb=" CA  THR U 111 "
        pdb=" CB  THR U 111 "
      ideal   model   delta    sigma   weight residual
     116.34  137.97  -21.63 1.40e+00 5.10e-01 2.39e+02
  ... (remaining 12861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.37: 5479
       24.37 -    48.75: 250
       48.75 -    73.12: 22
       73.12 -    97.49: 8
       97.49 -   121.87: 3
  Dihedral angle restraints: 5762
    sinusoidal: 2351
      harmonic: 3411
  Sorted by residual:
  dihedral pdb=" C   THR U1279 "
           pdb=" N   THR U1279 "
           pdb=" CA  THR U1279 "
           pdb=" CB  THR U1279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -98.92  -23.08     0      2.50e+00 1.60e-01 8.52e+01
  dihedral pdb=" C   ARG U 920 "
           pdb=" N   ARG U 920 "
           pdb=" CA  ARG U 920 "
           pdb=" CB  ARG U 920 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -100.02  -22.58     0      2.50e+00 1.60e-01 8.16e+01
  dihedral pdb=" N   MET U 921 "
           pdb=" C   MET U 921 "
           pdb=" CA  MET U 921 "
           pdb=" CB  MET U 921 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  102.72   20.08     0      2.50e+00 1.60e-01 6.45e+01
  ... (remaining 5759 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.194: 1441
       0.194 -    0.388: 27
       0.388 -    0.581: 1
       0.581 -    0.775: 3
       0.775 -    0.969: 1
  Chirality restraints: 1473
  Sorted by residual:
  chirality pdb=" CA  ARG U 920 "
            pdb=" N   ARG U 920 "
            pdb=" C   ARG U 920 "
            pdb=" CB  ARG U 920 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.54    0.97 2.00e-01 2.50e+01 2.35e+01
  chirality pdb=" CA  THR U1279 "
            pdb=" N   THR U1279 "
            pdb=" C   THR U1279 "
            pdb=" CB  THR U1279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    3.22   -0.69 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CA  ILE U 112 "
            pdb=" N   ILE U 112 "
            pdb=" C   ILE U 112 "
            pdb=" CB  ILE U 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.76    0.67 2.00e-01 2.50e+01 1.14e+01
  ... (remaining 1470 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 TCH U1401 "   -0.113 2.00e-02 2.50e+03   1.26e-01 1.99e+02
        pdb=" C24 TCH U1401 "    0.043 2.00e-02 2.50e+03
        pdb=" C25 TCH U1401 "   -0.153 2.00e-02 2.50e+03
        pdb=" N24 TCH U1401 "    0.203 2.00e-02 2.50e+03
        pdb=" O24 TCH U1401 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR U 769 "   -0.049 5.00e-02 4.00e+02   7.25e-02 8.42e+00
        pdb=" N   PRO U 770 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO U 770 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO U 770 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS U 969 "   -0.048 5.00e-02 4.00e+02   7.23e-02 8.35e+00
        pdb=" N   PRO U 970 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO U 970 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO U 970 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 57
        2.53 -     3.12: 6646
        3.12 -     3.71: 13788
        3.71 -     4.31: 18940
        4.31 -     4.90: 30840
  Nonbonded interactions: 70271
  Sorted by model distance:
  nonbonded pdb=" O   ARG U 920 "
            pdb=" CB  ARG U 920 "
     model   vdw
     1.936 2.752
  nonbonded pdb=" OD1 ASP U 350 "
            pdb=" N   GLU U 351 "
     model   vdw
     2.014 2.520
  nonbonded pdb=" N   THR U 111 "
            pdb=" O   THR U 111 "
     model   vdw
     2.079 2.496
  nonbonded pdb=" N   THR U1279 "
            pdb=" O   THR U1279 "
     model   vdw
     2.257 2.496
  nonbonded pdb=" C   SER U1278 "
            pdb=" O   THR U1279 "
     model   vdw
     2.272 3.270
  ... (remaining 70266 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          2.300
  Check model and map are aligned:         0.150
  Set scattering table:                    0.100
  Process input model:                     28.190
  Find NCS groups from input model:        0.280
  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:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.148   9503  Z= 0.674
  Angle     :  1.462  40.646  12866  Z= 0.824
  Chirality :  0.083   0.969   1473
  Planarity :  0.008   0.126   1632
  Dihedral  : 14.003 121.866   3572
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.73 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  8.81 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.55 %
  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: -6.60 (0.15), residues: 1185
  helix: -4.90 (0.07), residues: 634
  sheet: -4.65 (0.54), residues: 26
  loop : -3.52 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.003   TRP U 163 
   HIS   0.009   0.002   HIS U  72 
   PHE   0.026   0.003   PHE U 629 
   TYR   0.028   0.003   TYR U 981 
   ARG   0.014   0.001   ARG U1001 

*********************** 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
  211 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 10
  residues processed: 206
  average time/residue: 0.2729
  time to fit residues: 73.6847
Evaluate side-chains
  115 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.986 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1492
  time to fit residues: 3.7012
-------------------------------------------------------------------------------
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:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0670
   chunk 48 optimal weight:    6.9990
   chunk 93 optimal weight:    0.1980
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0030
   chunk 69 optimal weight:    3.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    0.6130

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

Flipped N/Q/H residues before XYZ refinement:
U 110 ASN
U 372 ASN
** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 867 GLN
U 946 ASN
U1097 ASN
U1107 GLN
U1258 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9503  Z= 0.164
  Angle     :  0.662   8.588  12866  Z= 0.336
  Chirality :  0.042   0.169   1473
  Planarity :  0.005   0.082   1632
  Dihedral  :  8.721 134.196   1433
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.46 %
    Favored  : 84.11 %
  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: -5.77 (0.17), residues: 1185
  helix: -4.17 (0.11), residues: 642
  sheet: -3.81 (0.67), residues: 26
  loop : -3.20 (0.23), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP U 493 
   HIS   0.005   0.001   HIS U1142 
   PHE   0.026   0.001   PHE U 925 
   TYR   0.019   0.001   TYR U1176 
   ARG   0.006   0.000   ARG U1001 

*********************** 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
  169 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 5
  residues processed: 163
  average time/residue: 0.2389
  time to fit residues: 53.3846
Evaluate side-chains
  117 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.995 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1431
  time to fit residues: 2.4298
-------------------------------------------------------------------------------
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:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 116 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
U 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9503  Z= 0.156
  Angle     :  0.611   9.886  12866  Z= 0.308
  Chirality :  0.041   0.142   1473
  Planarity :  0.003   0.038   1632
  Dihedral  :  8.285 135.463   1433
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.47 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.15 (0.19), residues: 1185
  helix: -3.57 (0.14), residues: 636
  sheet: -3.54 (0.67), residues: 26
  loop : -3.09 (0.23), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP U 846 
   HIS   0.003   0.001   HIS U1142 
   PHE   0.026   0.001   PHE U 925 
   TYR   0.012   0.001   TYR U1176 
   ARG   0.004   0.000   ARG U 920 

*********************** 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
  151 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.989 
Fit side-chains
  outliers start: 24
  outliers final: 11
  residues processed: 144
  average time/residue: 0.2340
  time to fit residues: 46.5750
Evaluate side-chains
  119 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.105 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1360
  time to fit residues: 3.8030
-------------------------------------------------------------------------------
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:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 51 optimal weight:   20.0000
   chunk 72 optimal weight:    8.9990
   chunk 108 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
U  72 HIS
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 563 GLN
U 640 HIS
** U 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.107   9503  Z= 0.720
  Angle     :  0.933   9.207  12866  Z= 0.481
  Chirality :  0.057   0.178   1473
  Planarity :  0.006   0.061   1632
  Dihedral  :  9.380 132.997   1433
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.14 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 16.19 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.30 (0.19), residues: 1185
  helix: -3.67 (0.14), residues: 653
  sheet: -4.26 (0.53), residues: 27
  loop : -3.09 (0.24), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.003   TRP U 846 
   HIS   0.006   0.002   HIS U  72 
   PHE   0.024   0.003   PHE U 427 
   TYR   0.026   0.003   TYR U 144 
   ARG   0.008   0.001   ARG U 832 

*********************** 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
  174 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 128
  time to evaluate  : 1.086 
Fit side-chains
  outliers start: 46
  outliers final: 23
  residues processed: 163
  average time/residue: 0.2170
  time to fit residues: 49.4771
Evaluate side-chains
  139 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.040 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1067
  time to fit residues: 5.6049
-------------------------------------------------------------------------------
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:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 58 optimal weight:    0.4980
   chunk 103 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
U 424 ASN
** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 946 ASN
** U1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9503  Z= 0.174
  Angle     :  0.634   8.503  12866  Z= 0.322
  Chirality :  0.042   0.141   1473
  Planarity :  0.003   0.037   1632
  Dihedral  :  8.436 134.752   1433
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.02 %
    Favored  : 79.76 %
  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: -4.75 (0.20), residues: 1185
  helix: -3.18 (0.16), residues: 644
  sheet: -3.73 (0.52), residues: 26
  loop : -2.94 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.001   TRP U 846 
   HIS   0.003   0.001   HIS U1142 
   PHE   0.023   0.001   PHE U 925 
   TYR   0.018   0.001   TYR U 538 
   ARG   0.003   0.000   ARG U 920 

*********************** 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
  144 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 9
  residues processed: 137
  average time/residue: 0.2344
  time to fit residues: 44.6607
Evaluate side-chains
  121 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 1.035 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0883
  time to fit residues: 2.9420
-------------------------------------------------------------------------------
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:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0010
   chunk 95 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 60 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9980
   overall best weight:    1.7390

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

Flipped N/Q/H residues before XYZ refinement:
U 946 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9503  Z= 0.206
  Angle     :  0.614  11.344  12866  Z= 0.312
  Chirality :  0.042   0.182   1473
  Planarity :  0.003   0.033   1632
  Dihedral  :  8.198 135.345   1433
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 19.43 %
    Favored  : 79.25 %
  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: -4.46 (0.21), residues: 1185
  helix: -2.89 (0.17), residues: 642
  sheet: -3.45 (0.55), residues: 26
  loop : -2.91 (0.24), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.001   TRP U 846 
   HIS   0.003   0.001   HIS U1142 
   PHE   0.019   0.001   PHE U 925 
   TYR   0.011   0.001   TYR U 337 
   ARG   0.004   0.000   ARG U 517 

*********************** 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
  136 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 5
  residues processed: 131
  average time/residue: 0.2531
  time to fit residues: 45.0010
Evaluate side-chains
  119 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.997 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1079
  time to fit residues: 2.3593
-------------------------------------------------------------------------------
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:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0770
   chunk 96 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 71 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 70 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.8340

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

Flipped N/Q/H residues before XYZ refinement:
U 424 ASN
U 563 GLN
U 946 ASN
** U1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.074   9503  Z= 0.156
  Angle     :  0.575   9.761  12866  Z= 0.293
  Chirality :  0.041   0.171   1473
  Planarity :  0.003   0.031   1632
  Dihedral  :  7.910 135.303   1433
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 20.75 %
    Favored  : 77.83 %
  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: -4.22 (0.21), residues: 1185
  helix: -2.60 (0.18), residues: 645
  sheet: -3.21 (0.61), residues: 26
  loop : -2.93 (0.24), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.001   TRP U 846 
   HIS   0.002   0.000   HIS U1142 
   PHE   0.017   0.001   PHE U 925 
   TYR   0.013   0.001   TYR U1005 
   ARG   0.002   0.000   ARG U 920 

*********************** 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
  143 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 3
  residues processed: 136
  average time/residue: 0.2387
  time to fit residues: 44.7683
Evaluate side-chains
  115 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.981 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1059
  time to fit residues: 2.0365
-------------------------------------------------------------------------------
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:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 109 optimal weight:   20.0000
   chunk 100 optimal weight:    5.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
U 484 HIS
U 563 GLN
U 946 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   9503  Z= 0.297
  Angle     :  0.632   9.491  12866  Z= 0.325
  Chirality :  0.044   0.166   1473
  Planarity :  0.003   0.035   1632
  Dihedral  :  8.092 134.885   1433
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 21.26 %
    Favored  : 77.33 %
  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: -4.18 (0.21), residues: 1185
  helix: -2.63 (0.18), residues: 642
  sheet: -3.38 (0.59), residues: 27
  loop : -2.81 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP U 752 
   HIS   0.002   0.001   HIS U1142 
   PHE   0.017   0.001   PHE U 925 
   TYR   0.014   0.002   TYR U 337 
   ARG   0.003   0.000   ARG U 832 

*********************** 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
  134 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 8
  residues processed: 127
  average time/residue: 0.2247
  time to fit residues: 39.6860
Evaluate side-chains
  120 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 1.005 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0864
  time to fit residues: 2.7027
-------------------------------------------------------------------------------
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:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0270
   chunk 32 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.0044

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

Flipped N/Q/H residues before XYZ refinement:
U 946 ASN
** U1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9503  Z= 0.160
  Angle     :  0.593   9.164  12866  Z= 0.301
  Chirality :  0.041   0.157   1473
  Planarity :  0.003   0.031   1632
  Dihedral  :  7.809 134.762   1433
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 21.86 %
    Favored  : 77.73 %
  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: -3.81 (0.22), residues: 1185
  helix: -2.35 (0.19), residues: 630
  sheet: -3.19 (0.64), residues: 27
  loop : -2.61 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP U 189 
   HIS   0.002   0.000   HIS U1142 
   PHE   0.016   0.001   PHE U 925 
   TYR   0.021   0.001   TYR U 538 
   ARG   0.002   0.000   ARG U 920 

*********************** 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
  127 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2629
  time to fit residues: 44.2129
Evaluate side-chains
  115 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.047 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4461
-------------------------------------------------------------------------------
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:    0.8980
   chunk 78 optimal weight:    0.0270
   chunk 118 optimal weight:    4.9990
   chunk 109 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0170
   chunk 74 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.9880

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

Flipped N/Q/H residues before XYZ refinement:
** U1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9503  Z= 0.220
  Angle     :  0.609   9.337  12866  Z= 0.310
  Chirality :  0.042   0.160   1473
  Planarity :  0.003   0.034   1632
  Dihedral  :  7.844 135.098   1433
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 22.67 %
    Favored  : 77.02 %
  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 (0.22), residues: 1185
  helix: -2.25 (0.19), residues: 638
  sheet: -3.14 (0.67), residues: 27
  loop : -2.70 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP U 752 
   HIS   0.002   0.001   HIS U1142 
   PHE   0.016   0.001   PHE U 925 
   TYR   0.018   0.001   TYR U 157 
   ARG   0.002   0.000   ARG U 637 

********************** 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
  123 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 122
  average time/residue: 0.2662
  time to fit residues: 44.1353
Evaluate side-chains
  118 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 1.087 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0886
  time to fit residues: 1.8286
-------------------------------------------------------------------------------
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:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
U 497 GLN
U 563 GLN
U1281 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.170032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127776 restraints weight = 12926.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.127890 restraints weight = 10232.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128410 restraints weight = 8130.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9503  Z= 0.150
  Angle     :  0.576   9.237  12866  Z= 0.292
  Chirality :  0.041   0.163   1473
  Planarity :  0.003   0.030   1632
  Dihedral  :  7.622 135.101   1433
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 22.67 %
    Favored  : 76.82 %
  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: -3.48 (0.22), residues: 1185
  helix: -2.05 (0.19), residues: 627
  sheet: -2.95 (0.71), residues: 27
  loop : -2.51 (0.25), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP U1071 
   HIS   0.002   0.000   HIS U1142 
   PHE   0.017   0.001   PHE U 427 
   TYR   0.016   0.001   TYR U1005 
   ARG   0.002   0.000   ARG U 792 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1957.38 seconds
wall clock time: 36 minutes 14.07 seconds (2174.07 seconds total)