Starting phenix.real_space_refine
on Fri Feb 14 00:44:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrc_21367/02_2025/6vrc_21367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrc_21367/02_2025/6vrc_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrc_21367/02_2025/6vrc_21367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrc_21367/02_2025/6vrc_21367.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrc_21367/02_2025/6vrc_21367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrc_21367/02_2025/6vrc_21367.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'ARG:plan': 1, 'HIS:plan': 2}
          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: 5.76, per 1000 atoms: 0.61
  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: 2.24
  Conformation dependent library (CDL) restraints added in 952.1 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: 2.92
  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: 3.42

  Time building geometry restraints manager: 2.61 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:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.970
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.780
-------------------------------------------------------------------------------
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= 0.622
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.83 (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
 TRP   0.029   0.004   TRP A 417 
 HIS   0.013   0.002   HIS A1093 
 PHE   0.034   0.003   PHE A1071 
 TYR   0.025   0.003   TYR A 486 
 ARG   0.024   0.002   ARG A  36 

*********************** 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  : 0.952 
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: 0.7202 (mt0)
  outliers start: 35
  outliers final: 9
  residues processed: 266
  average time/residue: 0.2446
  time to fit residues: 86.1894
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  : 0.942 
-------------------------------------------------------------------------------
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 88 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.148826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.117202 restraints weight = 13268.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.93
r_work: 0.3053 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9712  Z= 0.205
  Angle     :  0.684   9.992  13295  Z= 0.361
  Chirality :  0.043   0.253   1500
  Planarity :  0.005   0.058   1503
  Dihedral  : 17.508 175.697   1853
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.54 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.23), residues: 997
  helix: -1.78 (0.20), residues: 569
  sheet: -2.76 (0.83), residues: 27
  loop : -2.69 (0.26), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.026   0.002   PHE A 459 
 TYR   0.015   0.002   TYR A 889 
 ARG   0.005   0.001   ARG A  36 

*********************** 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  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7649 (t0)
REVERT: A  218 ASP cc_start: 0.8102 (t70) cc_final: 0.7824 (t0)
REVERT: A  383 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8947 (tp)
REVERT: A  514 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7255 (mmtm)
REVERT: A  820 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7754 (ttp80)
REVERT: A 1013 LYS cc_start: 0.7792 (tttt) cc_final: 0.7428 (tptt)
REVERT: A 1079 HIS cc_start: 0.8026 (m-70) cc_final: 0.7744 (m90)
REVERT: A 1086 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8780 (tt)
  outliers start: 34
  outliers final: 12
  residues processed: 174
  average time/residue: 0.2956
  time to fit residues: 66.7276
Evaluate side-chains
  115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
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  309 ASN
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  422 SER
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  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 43 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 97 optimal weight:    0.1980
   chunk 54 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 607 ASN
A1065 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.117551 restraints weight = 13350.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.96
r_work: 0.3061 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9712  Z= 0.160
  Angle     :  0.577   8.662  13295  Z= 0.303
  Chirality :  0.039   0.180   1500
  Planarity :  0.003   0.049   1503
  Dihedral  : 16.692 178.922   1832
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.03 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.25), residues: 997
  helix: -0.92 (0.22), residues: 568
  sheet: -2.69 (0.81), residues: 31
  loop : -2.46 (0.27), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.027   0.001   PHE A 459 
 TYR   0.012   0.001   TYR A 889 
 ARG   0.004   0.001   ARG A  36 

*********************** 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
  157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.8208 (t70) cc_final: 0.7920 (t0)
REVERT: A  342 GLU cc_start: 0.8427 (pp20) cc_final: 0.8137 (pp20)
REVERT: A  415 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8470 (ttp-110)
REVERT: A  459 PHE cc_start: 0.7426 (t80) cc_final: 0.7165 (t80)
REVERT: A  514 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7344 (mmtm)
REVERT: A  820 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7817 (ttp80)
REVERT: A  920 ASP cc_start: 0.8265 (m-30) cc_final: 0.7820 (m-30)
REVERT: A 1013 LYS cc_start: 0.7885 (tttt) cc_final: 0.7533 (tptt)
REVERT: A 1086 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8788 (tt)
  outliers start: 30
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2718
  time to fit residues: 53.8980
Evaluate side-chains
  115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
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  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  410 HIS
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  998 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 76 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 30 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 98 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 285 ASN
A 385 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.115358 restraints weight = 13144.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.99
r_work: 0.3032 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9712  Z= 0.170
  Angle     :  0.553   7.286  13295  Z= 0.290
  Chirality :  0.039   0.155   1500
  Planarity :  0.003   0.051   1503
  Dihedral  : 16.440 178.023   1830
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.66 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.25), residues: 997
  helix: -0.40 (0.22), residues: 581
  sheet: -2.74 (0.87), residues: 21
  loop : -2.35 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.020   0.001   PHE A 459 
 TYR   0.011   0.001   TYR A 889 
 ARG   0.004   0.001   ARG A  36 

*********************** 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
  157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8465 (mttt) cc_final: 0.8077 (ttmt)
REVERT: A  218 ASP cc_start: 0.8217 (t70) cc_final: 0.7926 (t0)
REVERT: A  415 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.8452 (ttp-110)
REVERT: A  484 PHE cc_start: 0.7931 (m-80) cc_final: 0.7703 (m-80)
REVERT: A  514 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7430 (mmtm)
REVERT: A  727 MET cc_start: 0.8450 (ttp) cc_final: 0.8200 (ttp)
REVERT: A  820 ARG cc_start: 0.8083 (ttp-110) cc_final: 0.7753 (ttp80)
REVERT: A  876 LYS cc_start: 0.7495 (mmtm) cc_final: 0.7086 (tttm)
REVERT: A  920 ASP cc_start: 0.8289 (m-30) cc_final: 0.7850 (m-30)
REVERT: A 1013 LYS cc_start: 0.7945 (tttt) cc_final: 0.7477 (tptt)
REVERT: A 1086 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8852 (tt)
  outliers start: 36
  outliers final: 15
  residues processed: 146
  average time/residue: 0.2755
  time to fit residues: 53.5605
Evaluate side-chains
  122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  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  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 1046 TYR
Chi-restraints excluded: chain A residue 1086 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 98 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0980
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    2.0188

-------------------------------------------------------------------------------
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 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.143608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110938 restraints weight = 13056.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.94
r_work: 0.2970 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9712  Z= 0.272
  Angle     :  0.610   6.805  13295  Z= 0.319
  Chirality :  0.042   0.156   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.301 177.954   1830
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.61 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.26), residues: 997
  helix: -0.24 (0.22), residues: 587
  sheet: -2.71 (0.87), residues: 19
  loop : -2.26 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 417 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.012   0.002   PHE A 604 
 TYR   0.012   0.002   TYR A 496 
 ARG   0.008   0.001   ARG A  36 

*********************** 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
  143 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8612 (mttt) cc_final: 0.8289 (ttmt)
REVERT: A  218 ASP cc_start: 0.8192 (t70) cc_final: 0.7915 (t0)
REVERT: A  415 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8349 (ttm110)
REVERT: A  507 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8698 (mt)
REVERT: A  514 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7490 (mmtm)
REVERT: A  621 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9187 (tp)
REVERT: A  727 MET cc_start: 0.8510 (ttp) cc_final: 0.8262 (ttp)
REVERT: A  768 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9060 (tp)
REVERT: A  794 MET cc_start: 0.8937 (tpp) cc_final: 0.8555 (ttm)
REVERT: A  876 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7346 (tptm)
REVERT: A 1013 LYS cc_start: 0.7908 (tttt) cc_final: 0.7448 (tptt)
  outliers start: 33
  outliers final: 17
  residues processed: 134
  average time/residue: 0.2904
  time to fit residues: 52.5856
Evaluate side-chains
  127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  295 ILE
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  621 LEU
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  998 LEU
Chi-restraints excluded: chain A residue 1046 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    2.0588

-------------------------------------------------------------------------------
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
A1093 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.143669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.111114 restraints weight = 13162.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.93
r_work: 0.2958 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9712  Z= 0.273
  Angle     :  0.594   6.498  13295  Z= 0.310
  Chirality :  0.042   0.151   1500
  Planarity :  0.004   0.049   1503
  Dihedral  : 16.247 177.759   1830
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.78 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.26), residues: 997
  helix: -0.05 (0.22), residues: 586
  sheet: -2.59 (0.89), residues: 21
  loop : -2.27 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 780 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.012   0.001   PHE A 604 
 TYR   0.013   0.002   TYR A 496 
 ARG   0.007   0.001   ARG A  36 

*********************** 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
  144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8699 (mttt) cc_final: 0.8420 (ttmt)
REVERT: A  218 ASP cc_start: 0.8221 (t70) cc_final: 0.7939 (t0)
REVERT: A  243 GLU cc_start: 0.7426 (mp0) cc_final: 0.7226 (mp0)
REVERT: A  415 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8335 (ttm110)
REVERT: A  507 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8687 (mt)
REVERT: A  514 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7421 (mmtm)
REVERT: A  605 THR cc_start: 0.9234 (m) cc_final: 0.7800 (t)
REVERT: A  727 MET cc_start: 0.8516 (ttp) cc_final: 0.8268 (ttp)
REVERT: A  753 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (p)
REVERT: A  768 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9033 (tp)
REVERT: A  820 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7923 (ttp80)
REVERT: A  876 LYS cc_start: 0.7788 (mmtm) cc_final: 0.7286 (tptm)
REVERT: A 1013 LYS cc_start: 0.7912 (tttt) cc_final: 0.7524 (tptt)
  outliers start: 33
  outliers final: 22
  residues processed: 133
  average time/residue: 0.2640
  time to fit residues: 47.1661
Evaluate side-chains
  125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  224 ILE
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  342 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  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  693 THR
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  998 LEU
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1074 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 101 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.143279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.111976 restraints weight = 13198.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.86
r_work: 0.2965 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9712  Z= 0.264
  Angle     :  0.599   8.853  13295  Z= 0.314
  Chirality :  0.042   0.149   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.186 177.813   1830
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.26), residues: 997
  helix:  0.03 (0.22), residues: 591
  sheet: -2.55 (0.75), residues: 35
  loop : -2.22 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 780 
 HIS   0.006   0.001   HIS A1093 
 PHE   0.011   0.001   PHE A 548 
 TYR   0.013   0.002   TYR A 496 
 ARG   0.007   0.000   ARG A  36 

*********************** 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
  138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8678 (mttt) cc_final: 0.8408 (ttmt)
REVERT: A  218 ASP cc_start: 0.8232 (t70) cc_final: 0.7950 (t0)
REVERT: A  415 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8489 (ttp-110)
REVERT: A  507 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8670 (mt)
REVERT: A  514 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7452 (mmtm)
REVERT: A  727 MET cc_start: 0.8528 (ttp) cc_final: 0.8265 (ttp)
REVERT: A  753 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7855 (p)
REVERT: A  768 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9036 (tp)
REVERT: A  820 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7942 (ttp80)
REVERT: A  876 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7247 (tptm)
REVERT: A  920 ASP cc_start: 0.8344 (m-30) cc_final: 0.7989 (m-30)
REVERT: A 1013 LYS cc_start: 0.7914 (tttt) cc_final: 0.7517 (tptt)
  outliers start: 34
  outliers final: 23
  residues processed: 128
  average time/residue: 0.2641
  time to fit residues: 45.3636
Evaluate side-chains
  128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
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  158 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  315 ILE
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  539 THR
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  693 THR
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 19 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 79 optimal weight:    0.3980
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0170
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.9620

-------------------------------------------------------------------------------
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
A 607 ASN
A 793 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.145687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.113657 restraints weight = 13253.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.98
r_work: 0.3021 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
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   0.036   9712  Z= 0.164
  Angle     :  0.530   8.138  13295  Z= 0.279
  Chirality :  0.039   0.139   1500
  Planarity :  0.003   0.048   1503
  Dihedral  : 16.021 178.066   1830
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.27), residues: 997
  helix:  0.36 (0.22), residues: 591
  sheet: -2.40 (0.92), residues: 19
  loop : -2.16 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 780 
 HIS   0.004   0.001   HIS A1093 
 PHE   0.013   0.001   PHE A 548 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A  36 

*********************** 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
  143 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7298 (tt0)
REVERT: A   98 LYS cc_start: 0.8638 (mttt) cc_final: 0.8340 (ttmt)
REVERT: A  218 ASP cc_start: 0.8243 (t70) cc_final: 0.7949 (t0)
REVERT: A  484 PHE cc_start: 0.7942 (m-80) cc_final: 0.7494 (m-80)
REVERT: A  507 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8614 (mt)
REVERT: A  514 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7441 (mmtm)
REVERT: A  534 GLU cc_start: 0.7679 (tp30) cc_final: 0.7423 (tp30)
REVERT: A  727 MET cc_start: 0.8526 (ttp) cc_final: 0.8257 (ttp)
REVERT: A  768 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8995 (tp)
REVERT: A  820 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7895 (ttp80)
REVERT: A  876 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7157 (tptm)
REVERT: A  920 ASP cc_start: 0.8261 (m-30) cc_final: 0.7793 (m-30)
REVERT: A 1013 LYS cc_start: 0.7889 (tttt) cc_final: 0.7498 (tptt)
  outliers start: 27
  outliers final: 17
  residues processed: 133
  average time/residue: 0.2644
  time to fit residues: 47.7237
Evaluate side-chains
  129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
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  124 ASN
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  342 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  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  693 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  998 LEU
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 19 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
A 607 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 = 0.145749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113395 restraints weight = 13148.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.95
r_work: 0.3006 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.5147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9712  Z= 0.195
  Angle     :  0.553   8.462  13295  Z= 0.290
  Chirality :  0.039   0.139   1500
  Planarity :  0.004   0.048   1503
  Dihedral  : 16.004 177.954   1830
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.27), residues: 997
  helix:  0.45 (0.22), residues: 594
  sheet: -2.38 (0.90), residues: 19
  loop : -2.16 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 780 
 HIS   0.004   0.001   HIS A1093 
 PHE   0.012   0.001   PHE A 548 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.004   0.000   ARG A  36 

*********************** 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
  135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.8205 (mmm) cc_final: 0.7867 (mmm)
REVERT: A   98 LYS cc_start: 0.8660 (mttt) cc_final: 0.8351 (ttmt)
REVERT: A  218 ASP cc_start: 0.8251 (t70) cc_final: 0.7957 (t0)
REVERT: A  507 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8625 (mt)
REVERT: A  514 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7435 (mmtm)
REVERT: A  534 GLU cc_start: 0.7716 (tp30) cc_final: 0.7432 (tp30)
REVERT: A  727 MET cc_start: 0.8525 (ttp) cc_final: 0.8264 (ttp)
REVERT: A  753 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7830 (p)
REVERT: A  768 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9005 (tp)
REVERT: A  820 ARG cc_start: 0.8245 (ttp-110) cc_final: 0.7921 (ttp80)
REVERT: A  876 LYS cc_start: 0.7788 (mmtm) cc_final: 0.7181 (tptm)
REVERT: A  920 ASP cc_start: 0.8302 (m-30) cc_final: 0.7859 (m-30)
REVERT: A 1013 LYS cc_start: 0.7879 (tttt) cc_final: 0.7507 (tptt)
REVERT: A 1086 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8863 (tt)
  outliers start: 26
  outliers final: 15
  residues processed: 127
  average time/residue: 0.2751
  time to fit residues: 46.4719
Evaluate side-chains
  126 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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  124 ASN
Chi-restraints excluded: chain A residue  158 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  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  693 THR
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  998 LEU
Chi-restraints excluded: chain A residue 1074 LEU
Chi-restraints excluded: chain A residue 1086 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 22 optimal weight:    0.1980
   chunk 66 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0030
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 101 HIS
A 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.146596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115493 restraints weight = 13178.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.91
r_work: 0.3028 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.5284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9712  Z= 0.150
  Angle     :  0.532   8.615  13295  Z= 0.278
  Chirality :  0.038   0.134   1500
  Planarity :  0.003   0.048   1503
  Dihedral  : 15.952 178.098   1830
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.58 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.27), residues: 997
  helix:  0.61 (0.23), residues: 593
  sheet: -2.28 (0.91), residues: 19
  loop : -2.14 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 456 
 HIS   0.004   0.001   HIS A1093 
 PHE   0.013   0.001   PHE A 548 
 TYR   0.010   0.001   TYR A1046 
 ARG   0.003   0.000   ARG A  36 

********************** 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
  134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8650 (mttt) cc_final: 0.8377 (ttmt)
REVERT: A  149 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7830 (ptt90)
REVERT: A  218 ASP cc_start: 0.8279 (t70) cc_final: 0.7953 (t0)
REVERT: A  484 PHE cc_start: 0.7868 (m-80) cc_final: 0.7444 (m-80)
REVERT: A  507 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8609 (mt)
REVERT: A  514 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7413 (mmtm)
REVERT: A  534 GLU cc_start: 0.7702 (tp30) cc_final: 0.7426 (tp30)
REVERT: A  727 MET cc_start: 0.8502 (ttp) cc_final: 0.8240 (ttp)
REVERT: A  753 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7864 (p)
REVERT: A  768 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9014 (tp)
REVERT: A  820 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7847 (ttp80)
REVERT: A  876 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7094 (tptm)
REVERT: A  920 ASP cc_start: 0.8280 (m-30) cc_final: 0.7815 (m-30)
REVERT: A 1013 LYS cc_start: 0.7865 (tttt) cc_final: 0.7510 (tptt)
REVERT: A 1086 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8849 (tt)
  outliers start: 24
  outliers final: 11
  residues processed: 128
  average time/residue: 0.2945
  time to fit residues: 49.8524
Evaluate side-chains
  127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
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  149 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  693 THR
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  802 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1086 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 31 optimal weight:    0.0060
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.1980
   chunk 64 optimal weight:    0.3980
   chunk 104 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.150285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118553 restraints weight = 13149.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.93
r_work: 0.3067 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.5457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9712  Z= 0.132
  Angle     :  0.508   8.682  13295  Z= 0.266
  Chirality :  0.037   0.132   1500
  Planarity :  0.003   0.051   1503
  Dihedral  : 15.864 177.829   1830
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.27), residues: 997
  helix:  0.85 (0.23), residues: 587
  sheet: -2.10 (0.92), residues: 19
  loop : -2.14 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 456 
 HIS   0.003   0.001   HIS A1093 
 PHE   0.012   0.001   PHE A 548 
 TYR   0.016   0.001   TYR A1046 
 ARG   0.002   0.000   ARG A  36 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4313.58 seconds
wall clock time: 77 minutes 29.84 seconds (4649.84 seconds total)