Starting phenix.real_space_refine
on Wed Mar  4 00:32:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrc_21367/03_2026/6vrc_21367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrc_21367/03_2026/6vrc_21367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrc_21367/03_2026/6vrc_21367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrc_21367/03_2026/6vrc_21367.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrc_21367/03_2026/6vrc_21367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrc_21367/03_2026/6vrc_21367.map"
  }
  resolution = 3.2
  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
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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      50      5.49       5
     S      28      5.16       5
     C    5822      2.51       5
     N    1603      2.21       5
     O    1926      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9429
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1007, 8359
          Classifications: {'peptide': 1007}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 23, 'TRANS': 983}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 1070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 1070
          Classifications: {'RNA': 51}
          Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 18, 'rna3p': 32}
  Time building chain proxies: 2.04, per 1000 atoms: 0.22
  Number of scatterers: 9429
  At special positions: 0
  Unit cell: (102.6, 92.88, 122.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      50     15.00
     O    1926      8.00
     N    1603      7.00
     C    5822      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 384.1 milliseconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 3 sheets defined
      58.1% alpha, 0.8% beta
      4 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 75
      removed outlier: 3.795A  pdb=" N   MET A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 85
      removed outlier: 3.611A  pdb=" N   ASN A  85 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 105
      removed outlier: 3.681A  pdb=" N   LEU A  99 " --> pdb=" O   GLN A  95 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   HIS A 101 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'A' and resid 153 through 163
      removed outlier: 3.946A  pdb=" N   SER A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
    Processing helix  chain 'A' and resid 179 through 203
      removed outlier: 3.613A  pdb=" N   ASN A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TRP A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS A 195 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS A 198 " --> pdb=" O   THR A 194 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ARG A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
      removed outlier: 3.573A  pdb=" N   LYS A 222 " --> pdb=" O   ASP A 218 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A 224 " --> pdb=" O   TYR A 220 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 225 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASN A 226 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 240
      removed outlier: 3.719A  pdb=" N   LYS A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 255
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.587A  pdb=" N   LYS A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A 269 " --> pdb=" O   TYR A 265 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   THR A 270 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLN A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE A 278 " --> pdb=" O   HIS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 287 through 303
      removed outlier: 3.605A  pdb=" N   LEU A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   THR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TYR A 302 " --> pdb=" O   HIS A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 332
      removed outlier: 3.764A  pdb=" N   LYS A 332 " --> pdb=" O   ASN A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 348
      removed outlier: 3.756A  pdb=" N   GLU A 342 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ALA A 346 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER A 347 " --> pdb=" O   GLY A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 388
      removed outlier: 3.582A  pdb=" N   ILE A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 367 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU A 370 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA A 375 " --> pdb=" O   LYS A 371 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   CYS A 376 " --> pdb=" O   PHE A 372 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 378 " --> pdb=" O   ASN A 374 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   MET A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 421
      removed outlier: 3.854A  pdb=" N   ILE A 414 " --> pdb=" O   HIS A 410 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG A 415 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLN A 419 " --> pdb=" O   ARG A 415 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE A 420 " --> pdb=" O   GLN A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
      removed outlier: 4.085A  pdb=" N   ARG A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY A 439 " --> pdb=" O   TRP A 435 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA A 440 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 500
      removed outlier: 4.242A  pdb=" N   ASP A 493 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 512
      removed outlier: 4.047A  pdb=" N   ILE A 507 " --> pdb=" O   PRO A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 524
    Processing helix  chain 'A' and resid 547 through 560
      removed outlier: 3.733A  pdb=" N   ASP A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 596
      removed outlier: 3.525A  pdb=" N   SER A 590 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET A 594 " --> pdb=" O   SER A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 607
      removed outlier: 4.478A  pdb=" N   GLN A 603 " --> pdb=" O   VAL A 599 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR A 606 " --> pdb=" O   PRO A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 623
      removed outlier: 3.574A  pdb=" N   PHE A 611 " --> pdb=" O   ASN A 607 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER A 614 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR A 620 " --> pdb=" O   ASP A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 658
      removed outlier: 4.187A  pdb=" N   SER A 649 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR A 650 " --> pdb=" O   GLU A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 665
      removed outlier: 4.007A  pdb=" N   LYS A 665 " --> pdb=" O   LYS A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 690
      removed outlier: 3.535A  pdb=" N   ILE A 675 " --> pdb=" O   PHE A 671 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLN A 677 " --> pdb=" O   LYS A 673 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 679 " --> pdb=" O   ILE A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 697
      removed outlier: 3.864A  pdb=" N   CYS A 696 " --> pdb=" O   THR A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 729
    Processing helix  chain 'A' and resid 733 through 748
      removed outlier: 3.727A  pdb=" N   SER A 737 " --> pdb=" O   ALA A 733 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 739 " --> pdb=" O   GLN A 735 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 745 " --> pdb=" O   ASN A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 763
      removed outlier: 3.816A  pdb=" N   PHE A 759 " --> pdb=" O   GLU A 755 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A 761 " --> pdb=" O   SER A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 773
      removed outlier: 3.532A  pdb=" N   LEU A 771 " --> pdb=" O   GLY A 767 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN A 772 " --> pdb=" O   LEU A 768 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY A 773 " --> pdb=" O   ALA A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 795
    Processing helix  chain 'A' and resid 819 through 828
      removed outlier: 3.686A  pdb=" N   LEU A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 825 " --> pdb=" O   SER A 821 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A 826 " --> pdb=" O   ILE A 822 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR A 828 " --> pdb=" O   LEU A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 838
    Processing helix  chain 'A' and resid 847 through 854
      removed outlier: 3.935A  pdb=" N   ILE A 851 " --> pdb=" O   SER A 847 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A 854 " --> pdb=" O   ASP A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 876
      removed outlier: 3.857A  pdb=" N   GLN A 865 " --> pdb=" O   GLU A 861 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TRP A 873 " --> pdb=" O   LEU A 869 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A 874 " --> pdb=" O   HIS A 870 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLU A 875 " --> pdb=" O   LYS A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 881
      removed outlier: 3.598A  pdb=" N   ARG A 881 " --> pdb=" O   GLY A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 907
      removed outlier: 3.697A  pdb=" N   LYS A 888 " --> pdb=" O   ALA A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 944
      removed outlier: 3.813A  pdb=" N   SER A 930 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ILE A 931 " --> pdb=" O   GLY A 927 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ASN A 941 " --> pdb=" O   GLN A 937 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   TYR A 942 " --> pdb=" O   PHE A 938 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE A 943 " --> pdb=" O   SER A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1003
    Processing helix  chain 'A' and resid 1011 through 1021
      removed outlier: 3.954A  pdb=" N   LYS A1015 " --> pdb=" O   ARG A1011 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A1019 " --> pdb=" O   LYS A1015 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER A1020 " --> pdb=" O   ARG A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1026
      removed outlier: 4.006A  pdb=" N   ASN A1026 " --> pdb=" O   ASN A1023 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1044
      removed outlier: 3.738A  pdb=" N   ARG A1041 " --> pdb=" O   PHE A1037 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASP A1042 " --> pdb=" O   ASP A1038 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A1043 " --> pdb=" O   ASP A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1047 through 1052
    Processing helix  chain 'A' and resid 1055 through 1065
      removed outlier: 3.713A  pdb=" N   LYS A1059 " --> pdb=" O   SER A1055 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU A1060 " --> pdb=" O   LYS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1118
      removed outlier: 3.592A  pdb=" N   CYS A1110 " --> pdb=" O   SER A1106 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN A1111 " --> pdb=" O   ASN A1107 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU A1112 " --> pdb=" O   GLU A1108 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 136
    Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465

    297 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      10 hydrogen bonds
      20 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 0.85 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: 1961
        1.33 -     1.45: 2434
        1.45 -     1.57: 5169
        1.57 -     1.69: 100
        1.69 -     1.81: 48
  Bond restraints: 9712
  Sorted by residual:
  bond pdb=" N   ILE A 112 "
       pdb=" CA  ILE A 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.11e-02 8.12e+03 1.27e+01
  bond pdb=" N   ILE A 515 "
       pdb=" CA  ILE A 515 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.25e-02 6.40e+03 1.22e+01
  bond pdb=" N   ILE A 263 "
       pdb=" CA  ILE A 263 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.21e-02 6.83e+03 9.48e+00
  bond pdb=" N   ILE A 320 "
       pdb=" CA  ILE A 320 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.22e-02 6.72e+03 9.40e+00
  bond pdb=" N   LEU A 601 "
       pdb=" CA  LEU A 601 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.04e-02 9.25e+03 9.26e+00
  ... (remaining 9707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 12032
        2.07 -     4.15: 1088
        4.15 -     6.22: 127
        6.22 -     8.29: 36
        8.29 -    10.37: 12
  Bond angle restraints: 13295
  Sorted by residual:
  angle pdb=" C3'   A B  34 "
        pdb=" C2'   A B  34 "
        pdb=" O2'   A B  34 "
      ideal   model   delta    sigma   weight residual
     114.60  124.79  -10.19 1.50e+00 4.44e-01 4.62e+01
  angle pdb=" N   GLU A 287 "
        pdb=" CA  GLU A 287 "
        pdb=" C   GLU A 287 "
      ideal   model   delta    sigma   weight residual
     113.88  105.87    8.01 1.23e+00 6.61e-01 4.24e+01
  angle pdb=" O3'   A B  34 "
        pdb=" C3'   A B  34 "
        pdb=" C2'   A B  34 "
      ideal   model   delta    sigma   weight residual
     109.50  118.71   -9.21 1.50e+00 4.44e-01 3.77e+01
  angle pdb=" C   CYS A  89 "
        pdb=" N   ARG A  90 "
        pdb=" CA  ARG A  90 "
      ideal   model   delta    sigma   weight residual
     120.09  127.70   -7.61 1.25e+00 6.40e-01 3.70e+01
  angle pdb=" N   SER A 247 "
        pdb=" CA  SER A 247 "
        pdb=" C   SER A 247 "
      ideal   model   delta    sigma   weight residual
     113.41  106.22    7.19 1.22e+00 6.72e-01 3.48e+01
  ... (remaining 13290 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 5769
       35.61 -    71.22: 199
       71.22 -   106.82: 20
      106.82 -   142.43: 2
      142.43 -   178.04: 4
  Dihedral angle restraints: 5994
    sinusoidal: 2982
      harmonic: 3012
  Sorted by residual:
  dihedral pdb=" O4'   U B  37 "
           pdb=" C1'   U B  37 "
           pdb=" N1    U B  37 "
           pdb=" C2    U B  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.68 -177.68     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B  12 "
           pdb=" C1'   U B  12 "
           pdb=" N1    U B  12 "
           pdb=" C2    U B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.87 -174.87     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   U B  33 "
           pdb=" C1'   U B  33 "
           pdb=" N1    U B  33 "
           pdb=" C2    U B  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -44.75 -115.25     1      1.50e+01 4.44e-03 6.09e+01
  ... (remaining 5991 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1310
       0.112 -    0.224: 174
       0.224 -    0.335: 10
       0.335 -    0.447: 3
       0.447 -    0.559: 3
  Chirality restraints: 1500
  Sorted by residual:
  chirality pdb=" C3'   G B   1 "
            pdb=" C4'   G B   1 "
            pdb=" O3'   G B   1 "
            pdb=" C2'   G B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.19   -0.56 2.00e-01 2.50e+01 7.81e+00
  chirality pdb=" C3'   A B  34 "
            pdb=" C4'   A B  34 "
            pdb=" O3'   A B  34 "
            pdb=" C2'   A B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.20   -0.54 2.00e-01 2.50e+01 7.32e+00
  chirality pdb=" C2'   A B  34 "
            pdb=" C3'   A B  34 "
            pdb=" O2'   A B  34 "
            pdb=" C1'   A B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.04   -0.48 2.00e-01 2.50e+01 5.65e+00
  ... (remaining 1497 not shown)

  Planarity restraints: 1503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 103 "    0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   LEU A 103 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   LEU A 103 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU A 104 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 822 "    0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   ILE A 822 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ILE A 822 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ASP A 823 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 607 "    0.016 2.00e-02 2.50e+03   3.15e-02 9.92e+00
        pdb=" C   ASN A 607 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ASN A 607 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN A 608 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1500 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 605
        2.72 -     3.26: 8559
        3.26 -     3.81: 14041
        3.81 -     4.35: 18699
        4.35 -     4.90: 30108
  Nonbonded interactions: 72012
  Sorted by model distance:
  nonbonded pdb=" O2'   C B   7 "
            pdb=" O5'   U B   8 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OE2 GLU A 498 "
            pdb=" ND2 ASN A 772 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OE2 GLU A 139 "
            pdb=" NZ  LYS A 195 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   ASN A 309 "
            pdb=" O6    G B   1 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   GLN A 523 "
            pdb=" OH  TYR A 694 "
     model   vdw
     2.274 3.040
  ... (remaining 72007 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             0.500
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.740
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
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      :  0.010   0.097   9712  Z= 0.542
  Angle     :  1.272  10.365  13295  Z= 0.794
  Chirality :  0.079   0.559   1500
  Planarity :  0.007   0.065   1503
  Dihedral  : 17.403 178.042   4028
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  :  8.99 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.83 (0.21), residues: 997
  helix: -3.25 (0.17), residues: 550
  sheet: -3.36 (0.60), residues: 38
  loop : -2.92 (0.25), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.002   ARG A  36 
 TYR   0.025   0.003   TYR A 486 
 PHE   0.034   0.003   PHE A1071 
 TRP   0.029   0.004   TRP A 417 
 HIS   0.013   0.002   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00994 ( 9712)
  covalent geometry    : angle       1.27191 (13295)
  hydrogen bonds       : bond        0.35762 (  307)
  hydrogen bonds       : angle       9.52308 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 245
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.7242 (m-70)
REVERT: A  218 ASP cc_start: 0.7939 (t70) cc_final: 0.7592 (t0)
REVERT: A  250 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (mtmm)
REVERT: A  338 ARG cc_start: 0.8151 (tpt-90) cc_final: 0.7937 (mtp85)
REVERT: A  586 GLN cc_start: 0.7422 (tt0) cc_final: 0.7201 (mt0)
  outliers start: 35
  outliers final: 9
  residues processed: 266
  average time/residue: 0.1107
  time to fit residues: 39.3624
Evaluate side-chains
  133 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  938 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  67 ASN
A 109 GLN
A 121 ASN
A 124 ASN
A 165 GLN
A 259 ASN
A 285 ASN
A 289 ASN
A 292 ASN
A 328 ASN
A 333 ASN
A 360 GLN
A 508 ASN
A 532 ASN
A 576 ASN
A 598 GLN
A 607 ASN
A 654 GLN
A 659 GLN
A 772 ASN
A 894 ASN
A 915 HIS
A1023 ASN
A1052 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.150329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118912 restraints weight = 13334.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.92
r_work: 0.3078 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9712  Z= 0.140
  Angle     :  0.666   9.877  13295  Z= 0.353
  Chirality :  0.042   0.263   1500
  Planarity :  0.005   0.057   1503
  Dihedral  : 17.526 176.061   1853
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.33 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.23), residues: 997
  helix: -1.78 (0.20), residues: 563
  sheet: -3.53 (0.62), residues: 19
  loop : -2.65 (0.26), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  90 
 TYR   0.016   0.001   TYR A 889 
 PHE   0.025   0.002   PHE A 459 
 TRP   0.017   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9712)
  covalent geometry    : angle       0.66611 (13295)
  hydrogen bonds       : bond        0.06640 (  307)
  hydrogen bonds       : angle       4.57135 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7653 (t0)
REVERT: A  153 ASN cc_start: 0.7590 (t0) cc_final: 0.7330 (t0)
REVERT: A  202 ARG cc_start: 0.8579 (mtt90) cc_final: 0.8336 (mtt180)
REVERT: A  218 ASP cc_start: 0.8081 (t70) cc_final: 0.7803 (t0)
REVERT: A  383 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8940 (tp)
REVERT: A  514 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7287 (mmtm)
REVERT: A  605 THR cc_start: 0.9067 (m) cc_final: 0.7577 (t)
REVERT: A  820 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7770 (ttp80)
REVERT: A 1079 HIS cc_start: 0.8007 (m-70) cc_final: 0.7730 (m90)
REVERT: A 1086 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8760 (tt)
  outliers start: 34
  outliers final: 9
  residues processed: 173
  average time/residue: 0.1253
  time to fit residues: 28.1448
Evaluate side-chains
  120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue 1074 LEU
Chi-restraints excluded: chain A residue 1086 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   chunk 85 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
A 207 GLN
A 416 GLN
A 461 ASN
A 586 GLN
A 607 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.144997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112845 restraints weight = 13209.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.98
r_work: 0.2990 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9712  Z= 0.178
  Angle     :  0.639   9.578  13295  Z= 0.334
  Chirality :  0.042   0.182   1500
  Planarity :  0.004   0.049   1503
  Dihedral  : 16.739 177.159   1832
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 14.92 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.25), residues: 997
  helix: -1.04 (0.21), residues: 576
  sheet: -2.81 (0.79), residues: 31
  loop : -2.51 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  36 
 TYR   0.013   0.002   TYR A 889 
 PHE   0.027   0.002   PHE A 459 
 TRP   0.012   0.002   TRP A 185 
 HIS   0.004   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 9712)
  covalent geometry    : angle       0.63897 (13295)
  hydrogen bonds       : bond        0.06639 (  307)
  hydrogen bonds       : angle       4.09340 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.8226 (t70) cc_final: 0.7937 (t0)
REVERT: A  412 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7533 (mmmt)
REVERT: A  415 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8499 (ttp-110)
REVERT: A  484 PHE cc_start: 0.7993 (m-80) cc_final: 0.7773 (m-80)
REVERT: A  514 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7445 (mmtm)
REVERT: A  820 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7827 (ttp80)
REVERT: A 1013 LYS cc_start: 0.7893 (tttt) cc_final: 0.7422 (tptt)
REVERT: A 1086 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8903 (tt)
  outliers start: 35
  outliers final: 18
  residues processed: 154
  average time/residue: 0.1163
  time to fit residues: 23.7592
Evaluate side-chains
  125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1074 LEU
Chi-restraints excluded: chain A residue 1086 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 105 GLN
A 124 ASN
A 165 GLN
A 385 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.142269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.111785 restraints weight = 13391.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.84
r_work: 0.2935 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9712  Z= 0.229
  Angle     :  0.666  11.433  13295  Z= 0.345
  Chirality :  0.044   0.172   1500
  Planarity :  0.004   0.051   1503
  Dihedral  : 16.662 177.767   1832
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 16.08 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.25), residues: 997
  helix: -0.70 (0.21), residues: 580
  sheet: -3.18 (0.68), residues: 39
  loop : -2.26 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  36 
 TYR   0.014   0.002   TYR A 496 
 PHE   0.029   0.002   PHE A 459 
 TRP   0.012   0.002   TRP A 417 
 HIS   0.005   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 9712)
  covalent geometry    : angle       0.66560 (13295)
  hydrogen bonds       : bond        0.06879 (  307)
  hydrogen bonds       : angle       4.09022 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.8397 (mmm) cc_final: 0.8173 (mmm)
REVERT: A  218 ASP cc_start: 0.8229 (t70) cc_final: 0.7947 (t0)
REVERT: A  415 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8453 (ttp-110)
REVERT: A  514 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7468 (mmtm)
REVERT: A  605 THR cc_start: 0.9240 (m) cc_final: 0.7749 (t)
REVERT: A  768 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9057 (tp)
REVERT: A  794 MET cc_start: 0.8891 (tpp) cc_final: 0.8508 (ttm)
REVERT: A  876 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7225 (tptm)
REVERT: A 1013 LYS cc_start: 0.7896 (tttt) cc_final: 0.7427 (tptt)
  outliers start: 39
  outliers final: 20
  residues processed: 137
  average time/residue: 0.1107
  time to fit residues: 20.3252
Evaluate side-chains
  122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  768 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1046 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
A 165 GLN
A 292 ASN
A1093 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.142028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.110580 restraints weight = 13210.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.88
r_work: 0.2950 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9712  Z= 0.198
  Angle     :  0.611   7.238  13295  Z= 0.319
  Chirality :  0.043   0.166   1500
  Planarity :  0.004   0.047   1503
  Dihedral  : 16.439 177.589   1832
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.26), residues: 997
  helix: -0.40 (0.21), residues: 584
  sheet: -3.24 (0.66), residues: 41
  loop : -2.24 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  36 
 TYR   0.013   0.002   TYR A 496 
 PHE   0.031   0.002   PHE A 459 
 TRP   0.011   0.002   TRP A 417 
 HIS   0.005   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9712)
  covalent geometry    : angle       0.61065 (13295)
  hydrogen bonds       : bond        0.06302 (  307)
  hydrogen bonds       : angle       3.96502 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.8390 (mmm) cc_final: 0.8156 (mmm)
REVERT: A  218 ASP cc_start: 0.8227 (t70) cc_final: 0.7945 (t0)
REVERT: A  415 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8488 (ttp-110)
REVERT: A  507 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8717 (mt)
REVERT: A  514 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7451 (mmtm)
REVERT: A  753 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7994 (p)
REVERT: A  768 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9063 (tp)
REVERT: A  876 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7154 (tttm)
REVERT: A 1013 LYS cc_start: 0.7962 (tttt) cc_final: 0.7471 (tptt)
REVERT: A 1086 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8923 (tt)
  outliers start: 36
  outliers final: 20
  residues processed: 135
  average time/residue: 0.1117
  time to fit residues: 20.1375
Evaluate side-chains
  123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  753 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  768 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1086 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
A 165 GLN
A 607 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.143130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.110796 restraints weight = 13112.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.94
r_work: 0.2948 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9712  Z= 0.183
  Angle     :  0.590   6.939  13295  Z= 0.309
  Chirality :  0.042   0.155   1500
  Planarity :  0.004   0.050   1503
  Dihedral  : 16.335 177.857   1832
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 16.93 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.26), residues: 997
  helix: -0.12 (0.22), residues: 587
  sheet: -2.35 (0.70), residues: 45
  loop : -2.19 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  36 
 TYR   0.011   0.001   TYR A 496 
 PHE   0.011   0.001   PHE A 548 
 TRP   0.010   0.002   TRP A 417 
 HIS   0.006   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9712)
  covalent geometry    : angle       0.59007 (13295)
  hydrogen bonds       : bond        0.06040 (  307)
  hydrogen bonds       : angle       3.90073 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.8328 (mmm) cc_final: 0.8076 (mmm)
REVERT: A  218 ASP cc_start: 0.8232 (t70) cc_final: 0.7939 (t0)
REVERT: A  415 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8485 (ttp-110)
REVERT: A  507 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8707 (mt)
REVERT: A  514 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7415 (mmtm)
REVERT: A  727 MET cc_start: 0.8536 (ttp) cc_final: 0.8278 (ttp)
REVERT: A  753 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8011 (p)
REVERT: A  768 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8998 (tp)
REVERT: A  794 MET cc_start: 0.8906 (tpp) cc_final: 0.8613 (ttm)
REVERT: A  820 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7897 (ttp80)
REVERT: A  876 LYS cc_start: 0.7531 (mmtm) cc_final: 0.7056 (tttm)
REVERT: A 1013 LYS cc_start: 0.7899 (tttt) cc_final: 0.7487 (tptt)
  outliers start: 40
  outliers final: 23
  residues processed: 142
  average time/residue: 0.1136
  time to fit residues: 21.8771
Evaluate side-chains
  130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  753 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  768 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1046 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
A 165 GLN
A 607 ASN
A 772 ASN
A 793 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.110617 restraints weight = 13165.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.83
r_work: 0.2945 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9712  Z= 0.199
  Angle     :  0.608   7.013  13295  Z= 0.319
  Chirality :  0.043   0.155   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.310 177.921   1832
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.78 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.26), residues: 997
  helix: -0.05 (0.22), residues: 590
  sheet: -2.56 (0.64), residues: 51
  loop : -2.23 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  36 
 TYR   0.013   0.002   TYR A 496 
 PHE   0.035   0.002   PHE A 459 
 TRP   0.011   0.002   TRP A 417 
 HIS   0.004   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 9712)
  covalent geometry    : angle       0.60788 (13295)
  hydrogen bonds       : bond        0.06241 (  307)
  hydrogen bonds       : angle       3.92054 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A   96 MET cc_start: 0.8403 (mmm) cc_final: 0.8094 (mmt)
REVERT: A  218 ASP cc_start: 0.8288 (t70) cc_final: 0.7993 (t0)
REVERT: A  415 ARG cc_start: 0.8821 (mtm-85) cc_final: 0.8502 (ttp-110)
REVERT: A  507 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8709 (mt)
REVERT: A  514 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7431 (mmtm)
REVERT: A  605 THR cc_start: 0.9232 (m) cc_final: 0.7816 (t)
REVERT: A  727 MET cc_start: 0.8564 (ttp) cc_final: 0.8299 (ttp)
REVERT: A  753 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8064 (p)
REVERT: A  768 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9075 (tp)
REVERT: A  794 MET cc_start: 0.8800 (tpp) cc_final: 0.8464 (ttm)
REVERT: A  820 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7910 (ttp80)
REVERT: A  876 LYS cc_start: 0.7558 (mmtm) cc_final: 0.7084 (tttm)
REVERT: A 1013 LYS cc_start: 0.7933 (tttt) cc_final: 0.7503 (tptt)
  outliers start: 37
  outliers final: 25
  residues processed: 134
  average time/residue: 0.1168
  time to fit residues: 21.2030
Evaluate side-chains
  133 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  753 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  768 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1074 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 82 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.143205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.111075 restraints weight = 13235.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.92
r_work: 0.2980 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9712  Z= 0.144
  Angle     :  0.554   6.483  13295  Z= 0.293
  Chirality :  0.040   0.146   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.191 178.175   1832
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.52 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.27), residues: 997
  helix:  0.19 (0.22), residues: 590
  sheet: -1.96 (0.76), residues: 41
  loop : -2.18 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  36 
 TYR   0.010   0.001   TYR A 496 
 PHE   0.037   0.001   PHE A 459 
 TRP   0.010   0.001   TRP A 456 
 HIS   0.004   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9712)
  covalent geometry    : angle       0.55444 (13295)
  hydrogen bonds       : bond        0.05388 (  307)
  hydrogen bonds       : angle       3.74873 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7701 (tt0)
REVERT: A  218 ASP cc_start: 0.8265 (t70) cc_final: 0.7966 (t0)
REVERT: A  415 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8489 (ttp-110)
REVERT: A  484 PHE cc_start: 0.8093 (m-80) cc_final: 0.7614 (m-80)
REVERT: A  507 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8683 (mt)
REVERT: A  514 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7413 (mmtm)
REVERT: A  727 MET cc_start: 0.8513 (ttp) cc_final: 0.8225 (ttp)
REVERT: A  753 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7981 (p)
REVERT: A  768 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9021 (tp)
REVERT: A  794 MET cc_start: 0.8820 (tpp) cc_final: 0.8430 (ttm)
REVERT: A  820 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7853 (ttp80)
REVERT: A  876 LYS cc_start: 0.7506 (mmtm) cc_final: 0.7062 (tttm)
REVERT: A 1013 LYS cc_start: 0.7888 (tttt) cc_final: 0.7482 (tptt)
  outliers start: 32
  outliers final: 21
  residues processed: 133
  average time/residue: 0.1176
  time to fit residues: 20.9760
Evaluate side-chains
  130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  753 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  768 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1074 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.142644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110243 restraints weight = 13210.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.93
r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.5120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9712  Z= 0.171
  Angle     :  0.592   9.770  13295  Z= 0.308
  Chirality :  0.041   0.152   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.183 178.182   1832
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.52 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.27), residues: 997
  helix:  0.23 (0.22), residues: 590
  sheet: -1.92 (0.70), residues: 45
  loop : -2.20 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  36 
 TYR   0.012   0.001   TYR A 496 
 PHE   0.034   0.002   PHE A 459 
 TRP   0.010   0.001   TRP A 417 
 HIS   0.004   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 9712)
  covalent geometry    : angle       0.59249 (13295)
  hydrogen bonds       : bond        0.05819 (  307)
  hydrogen bonds       : angle       3.79609 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7658 (tt0)
REVERT: A  218 ASP cc_start: 0.8265 (t70) cc_final: 0.7966 (t0)
REVERT: A  243 GLU cc_start: 0.7416 (mp0) cc_final: 0.7203 (mp0)
REVERT: A  415 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.8494 (ttp-110)
REVERT: A  507 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8690 (mt)
REVERT: A  514 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7431 (mmtm)
REVERT: A  605 THR cc_start: 0.9216 (m) cc_final: 0.7814 (t)
REVERT: A  727 MET cc_start: 0.8524 (ttp) cc_final: 0.8243 (ttp)
REVERT: A  753 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (p)
REVERT: A  768 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9034 (tp)
REVERT: A  794 MET cc_start: 0.8847 (tpp) cc_final: 0.8458 (ttm)
REVERT: A  820 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7829 (ttp80)
REVERT: A  876 LYS cc_start: 0.7549 (mmtm) cc_final: 0.7100 (tttm)
REVERT: A 1013 LYS cc_start: 0.7866 (tttt) cc_final: 0.7440 (tptt)
  outliers start: 31
  outliers final: 25
  residues processed: 130
  average time/residue: 0.1137
  time to fit residues: 19.8843
Evaluate side-chains
  135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  753 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  768 LEU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1074 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 86 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
A 285 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.145588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113881 restraints weight = 13118.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.91
r_work: 0.3012 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9712  Z= 0.116
  Angle     :  0.546   9.633  13295  Z= 0.284
  Chirality :  0.039   0.142   1500
  Planarity :  0.003   0.047   1503
  Dihedral  : 16.047 178.115   1832
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.58 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.27), residues: 997
  helix:  0.53 (0.23), residues: 591
  sheet: -1.46 (0.82), residues: 31
  loop : -2.17 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  44 
 TYR   0.008   0.001   TYR A1109 
 PHE   0.039   0.001   PHE A 459 
 TRP   0.010   0.001   TRP A 456 
 HIS   0.003   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9712)
  covalent geometry    : angle       0.54586 (13295)
  hydrogen bonds       : bond        0.04650 (  307)
  hydrogen bonds       : angle       3.57301 (  878)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.8251 (t70) cc_final: 0.7915 (t0)
REVERT: A  232 ASP cc_start: 0.7002 (t70) cc_final: 0.6478 (t70)
REVERT: A  415 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8484 (ttp-110)
REVERT: A  484 PHE cc_start: 0.7979 (m-80) cc_final: 0.7606 (m-80)
REVERT: A  507 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8663 (mt)
REVERT: A  514 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7564 (mmtm)
REVERT: A  727 MET cc_start: 0.8534 (ttp) cc_final: 0.8272 (ttp)
REVERT: A  753 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7867 (p)
REVERT: A  820 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7881 (ttp80)
REVERT: A  876 LYS cc_start: 0.7331 (mmtm) cc_final: 0.7037 (tptm)
REVERT: A  920 ASP cc_start: 0.8261 (m-30) cc_final: 0.7787 (m-30)
REVERT: A 1013 LYS cc_start: 0.7888 (tttt) cc_final: 0.7497 (tptt)
  outliers start: 23
  outliers final: 14
  residues processed: 137
  average time/residue: 0.1235
  time to fit residues: 22.5780
Evaluate side-chains
  123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  753 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1074 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 89 optimal weight:    0.0040
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.5596

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 124 ASN
A 894 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.142794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.111163 restraints weight = 13100.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.90
r_work: 0.2975 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.5294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9712  Z= 0.156
  Angle     :  0.590   9.505  13295  Z= 0.307
  Chirality :  0.041   0.142   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.075 178.258   1832
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.11 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.27), residues: 997
  helix:  0.49 (0.22), residues: 592
  sheet: -1.49 (0.81), residues: 31
  loop : -2.11 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  36 
 TYR   0.010   0.001   TYR A 496 
 PHE   0.041   0.001   PHE A 459 
 TRP   0.009   0.001   TRP A 417 
 HIS   0.004   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9712)
  covalent geometry    : angle       0.59034 (13295)
  hydrogen bonds       : bond        0.05452 (  307)
  hydrogen bonds       : angle       3.69411 (  878)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2105.37 seconds
wall clock time: 36 minutes 53.46 seconds (2213.46 seconds total)