Starting phenix.real_space_refine
on Fri Aug  7 02:25:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cjj_45633/08_2026/9cjj_45633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cjj_45633/08_2026/9cjj_45633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cjj_45633/08_2026/9cjj_45633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cjj_45633/08_2026/9cjj_45633.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cjj_45633/08_2026/9cjj_45633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cjj_45633/08_2026/9cjj_45633.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9408 atoms to isotropic.
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      57      5.49       5
     S      27      5.16       5
     C    7001      2.51       5
     N    1922      2.21       5
     O    2233      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11240
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 528
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 5, 'rna3p': 19}
    Chain: "A"
      Number of atoms: 10051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1240, 10051
          Classifications: {'peptide': 1240}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 46, 'TRANS': 1193}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 84
          Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "C"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 105
          Classifications: {'DNA': 5}
          Link IDs: {'rna3p': 4}
    Chain: "C"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 204
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 352
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 15, 309
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
      Conformer: "B"
        Number of residues, atoms: 15, 309
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
          bond proxies already assigned to first conformer: 298
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" P  A DG D  19 " occ=0.90
      ... (42 atoms not shown)
      pdb=" C4 B DG D  19 " occ=0.10
    residue:
      pdb=" P  A DA D  20 " occ=0.90
      ... (40 atoms not shown)
      pdb=" C4 B DA D  20 " occ=0.10
  Time building chain proxies: 2.88, per 1000 atoms: 0.26
  Number of scatterers: 11240
  At special positions: 0
  Unit cell: (98.12, 110.385, 138.26, 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      27     16.00
     P      57     15.00
     O    2233      8.00
     N    1922      7.00
     C    7001      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 486.7 milliseconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2370

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 9 sheets defined
      56.1% alpha, 10.3% beta
      17 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 35 through 50
    Processing helix  chain 'A' and resid 50 through 68
      removed outlier: 4.277A  pdb=" N   TYR A  61 " --> pdb=" O   ILE A  57 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU A  68 " --> pdb=" O   GLN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 86
    Processing helix  chain 'A' and resid 88 through 112
      removed outlier: 3.823A  pdb=" N   TYR A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 131
      removed outlier: 3.750A  pdb=" N   ALA A 126 " --> pdb=" O   ASN A 122 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE A 128 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 133
      No H-bonds generated for 'chain 'A' and resid 132 through 133'
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 140 through 146
    Processing helix  chain 'A' and resid 152 through 160
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 169 through 181
      removed outlier: 3.523A  pdb=" N   GLU A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL A 179 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 196
      removed outlier: 3.529A  pdb=" N   ASP A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 215
      removed outlier: 3.787A  pdb=" N   LYS A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 230
      removed outlier: 4.235A  pdb=" N   GLU A 220 " --> pdb=" O   PRO A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 249
    Processing helix  chain 'A' and resid 251 through 264
    Processing helix  chain 'A' and resid 325 through 344
      removed outlier: 4.068A  pdb=" N   VAL A 329 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 330 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ARG A 341 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN A 342 " --> pdb=" O   THR A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.548A  pdb=" N   LEU A 356 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
      removed outlier: 3.729A  pdb=" N   HIS A 363 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 367 through 379
      removed outlier: 4.678A  pdb=" N   GLU A 372 " --> pdb=" O   HIS A 368 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   THR A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 395
      removed outlier: 4.626A  pdb=" N   ARG A 386 " --> pdb=" O   TRP A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 415
      removed outlier: 3.566A  pdb=" N   LYS A 414 " --> pdb=" O   GLN A 410 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   HIS A 415 " --> pdb=" O   ARG A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 428
    Processing helix  chain 'A' and resid 428 through 451
      removed outlier: 4.167A  pdb=" N   SER A 432 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASP A 451 " --> pdb=" O   HIS A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      removed outlier: 3.657A  pdb=" N   ILE A 466 " --> pdb=" O   GLU A 462 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASP A 482 " --> pdb=" O   TYR A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 523
      Proline residue:  A 509  - end of helix
      removed outlier: 3.956A  pdb=" N   ASN A 515 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 547
      No H-bonds generated for 'chain 'A' and resid 545 through 547'
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 570 through 574
    Processing helix  chain 'A' and resid 600 through 610
      Proline residue:  A 606  - end of helix
    Processing helix  chain 'A' and resid 612 through 622
    Processing helix  chain 'A' and resid 639 through 647
      removed outlier: 3.828A  pdb=" N   TYR A 643 " --> pdb=" O   THR A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 663
    Processing helix  chain 'A' and resid 665 through 687
    Processing helix  chain 'A' and resid 700 through 704
      removed outlier: 3.564A  pdb=" N   GLN A 703 " --> pdb=" O   PRO A 700 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 704 " --> pdb=" O   SER A 701 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 700 through 704'
    Processing helix  chain 'A' and resid 706 through 719
      removed outlier: 3.627A  pdb=" N   TYR A 710 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      Proline residue:  A 716  - end of helix
      removed outlier: 3.789A  pdb=" N   TYR A 719 " --> pdb=" O   ASN A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 738
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.616A  pdb=" N   PHE A 769 " --> pdb=" O   TRP A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
    Processing helix  chain 'A' and resid 819 through 831
      removed outlier: 3.567A  pdb=" N   GLN A 824 " --> pdb=" O   ASP A 820 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU A 825 " --> pdb=" O   THR A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 846
    Processing helix  chain 'A' and resid 861 through 865
    Processing helix  chain 'A' and resid 887 through 899
      removed outlier: 3.570A  pdb=" N   ARG A 891 " --> pdb=" O   LYS A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 943 through 955
    Processing helix  chain 'A' and resid 957 through 987
      removed outlier: 3.970A  pdb=" N   VAL A 961 " --> pdb=" O   ALA A 957 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   HIS A 977 " --> pdb=" O   SER A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1025
      removed outlier: 3.944A  pdb=" N   CYS A1025 " --> pdb=" O   ASP A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.527A  pdb=" N   THR A1087 " --> pdb=" O   VAL A1084 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE A1088 " --> pdb=" O   TRP A1085 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1084 through 1088'
    Processing helix  chain 'A' and resid 1090 through 1100
    Processing helix  chain 'A' and resid 1177 through 1190
    Processing helix  chain 'A' and resid 1199 through 1207
      removed outlier: 3.569A  pdb=" N   ASP A1207 " --> pdb=" O   LEU A1203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1223
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1261 through 1284
      removed outlier: 3.744A  pdb=" N   GLY A1266 " --> pdb=" O   ALA A1262 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A1267 " --> pdb=" O   ASP A1263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1306
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532
      removed outlier: 3.970A  pdb=" N   PHE A 869 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   TYR A 563 " --> pdb=" O   ILE A 745 " (cutoff:3.500A)
      removed outlier: 11.270A  pdb=" N   ALA A 554 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 8.673A  pdb=" N   TYR A 595 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LEU A 556 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628
    Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 811
      removed outlier: 5.233A  pdb=" N   ILE A 850 " --> pdb=" O   ASN A 808 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931
      removed outlier: 3.703A  pdb=" N   GLU A 928 " --> pdb=" O   VAL A 919 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ILE A 905 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   GLU A 993 " --> pdb=" O   ILE A 905 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   ILE A 907 " --> pdb=" O   GLU A 993 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1103 through 1106
      removed outlier: 3.876A  pdb=" N   PHE A1103 " --> pdb=" O   HIS A1116 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1161

    516 hydrogen bonds defined for protein.
    1446 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      40 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 1.48 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: 3043
        1.33 -     1.46: 2456
        1.46 -     1.58: 5955
        1.58 -     1.70: 111
        1.70 -     1.82: 44
  Bond restraints: 11609
  Sorted by residual:
  bond pdb=" O5' 2YR C   7 "
       pdb=" P   2YR C   7 "
    ideal  model  delta    sigma   weight residual
    1.721  1.600  0.121 2.00e-02 2.50e+03 3.65e+01
  bond pdb=" C3'  DG C   6 "
       pdb=" C2'  DG C   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.08e+01
  bond pdb=" C3'  DT C  12 "
       pdb=" C2'  DT C  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" N   ILE A  57 "
       pdb=" CA  ILE A  57 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.00e+01
  bond pdb=" C3'  DC D  21 "
       pdb=" C2'  DC D  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.67e+00
  ... (remaining 11604 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 15564
        1.80 -     3.60: 339
        3.60 -     5.40: 34
        5.40 -     7.19: 4
        7.19 -     8.99: 4
  Bond angle restraints: 15945
  Sorted by residual:
  angle pdb=" N   TYR A  58 "
        pdb=" CA  TYR A  58 "
        pdb=" C   TYR A  58 "
      ideal   model   delta    sigma   weight residual
     113.50  105.11    8.39 1.23e+00 6.61e-01 4.66e+01
  angle pdb=" C   LYS A  59 "
        pdb=" N   THR A  60 "
        pdb=" CA  THR A  60 "
      ideal   model   delta    sigma   weight residual
     120.54  112.09    8.45 1.35e+00 5.49e-01 3.91e+01
  angle pdb=" O4'  DA C   3 "
        pdb=" C4'  DA C   3 "
        pdb=" C3'  DA C   3 "
      ideal   model   delta    sigma   weight residual
     106.00  103.20    2.80 6.00e-01 2.78e+00 2.17e+01
  angle pdb=" N   LEU A 505 "
        pdb=" CA  LEU A 505 "
        pdb=" C   LEU A 505 "
      ideal   model   delta    sigma   weight residual
     112.34  106.74    5.60 1.30e+00 5.92e-01 1.86e+01
  angle pdb=" N3   DT C  10 "
        pdb=" C4   DT C  10 "
        pdb=" O4   DT C  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.42   -2.52 6.00e-01 2.78e+00 1.76e+01
  ... (remaining 15940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 6598
       35.61 -    71.21: 313
       71.21 -   106.82: 16
      106.82 -   142.42: 3
      142.42 -   178.03: 2
  Dihedral angle restraints: 6932
    sinusoidal: 3270
      harmonic: 3662
  Sorted by residual:
  dihedral pdb=" O4'   U B  16 "
           pdb=" C1'   U B  16 "
           pdb=" N1    U B  16 "
           pdb=" C2    U B  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   58.88  173.12     1      1.70e+01 3.46e-03 6.62e+01
  dihedral pdb=" C4'A DG D  19 "
           pdb=" C3'A DG D  19 "
           pdb=" O3'A DG D  19 "
           pdb=" P  A DA D  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.03 -178.03     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  ASP A 383 "
           pdb=" C   ASP A 383 "
           pdb=" N   THR A 384 "
           pdb=" CA  THR A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.52  -18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 6929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1363
       0.045 -    0.090: 306
       0.090 -    0.134: 89
       0.134 -    0.179: 13
       0.179 -    0.224: 4
  Chirality restraints: 1775
  Sorted by residual:
  chirality pdb=" CA  TYR A  58 "
            pdb=" N   TYR A  58 "
            pdb=" C   TYR A  58 "
            pdb=" CB  TYR A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" C1' 2YR C   7 "
            pdb=" C2' 2YR C   7 "
            pdb=" N1  2YR C   7 "
            pdb=" O4' 2YR C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.24    2.45   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE A  57 "
            pdb=" N   ILE A  57 "
            pdb=" C   ILE A  57 "
            pdb=" CB  ILE A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1772 not shown)

  Planarity restraints: 1842
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' 2YR C   7 "    0.088 2.00e-02 2.50e+03   1.38e-01 4.74e+02
        pdb=" C2  2YR C   7 "    0.018 2.00e-02 2.50e+03
        pdb=" C4  2YR C   7 "   -0.118 2.00e-02 2.50e+03
        pdb=" C5  2YR C   7 "   -0.124 2.00e-02 2.50e+03
        pdb=" C6  2YR C   7 "   -0.059 2.00e-02 2.50e+03
        pdb=" C9  2YR C   7 "    0.326 2.00e-02 2.50e+03
        pdb=" N1  2YR C   7 "    0.013 2.00e-02 2.50e+03
        pdb=" N3  2YR C   7 "   -0.049 2.00e-02 2.50e+03
        pdb=" N4  2YR C   7 "   -0.180 2.00e-02 2.50e+03
        pdb=" O2  2YR C   7 "    0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 502 "    0.013 2.00e-02 2.50e+03   2.45e-02 6.02e+00
        pdb=" C   GLY A 502 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLY A 502 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A 503 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 916 "    0.007 2.00e-02 2.50e+03   1.23e-02 3.04e+00
        pdb=" CG  TYR A 916 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 916 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 916 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 916 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 916 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 916 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 916 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1839 not shown)

  Histogram of nonbonded interaction distances:
        0.45 -     1.34: 4
        1.34 -     2.23: 26
        2.23 -     3.12: 8423
        3.12 -     4.01: 30078
        4.01 -     4.90: 54642
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 93173
  Sorted by model distance:
  nonbonded pdb=" CG  ARG A  43 "
            pdb=" O   SER A 161 "
     model   vdw
     0.454 3.440
  nonbonded pdb=" CB  TYR A  47 "
            pdb=" CE2 PHE A 162 "
     model   vdw
     0.754 3.740
  nonbonded pdb=" CB  TYR A  47 "
            pdb=" CZ  PHE A 162 "
     model   vdw
     1.072 3.740
  nonbonded pdb=" CE2 PHE A 165 "
            pdb=" CG  LYS A 532 "
     model   vdw
     1.331 3.740
  nonbonded pdb=" CD  ARG A  43 "
            pdb=" O   SER A 161 "
     model   vdw
     1.355 3.440
  ... (remaining 93168 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=0.10 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.560
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
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      :  0.003   0.121  11611  Z= 0.236
  Angle     :  0.589   8.993  15945  Z= 0.393
  Chirality :  0.043   0.224   1775
  Planarity :  0.005   0.138   1842
  Dihedral  : 18.201 178.027   4562
  Min Nonbonded Distance : 0.454

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  1.84 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.24), residues: 1232
  helix: -0.39 (0.20), residues: 583
  sheet: -0.49 (0.44), residues: 147
  loop : -0.11 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1003 
 TYR   0.027   0.001   TYR A 916 
 PHE   0.019   0.001   PHE A1154 
 TRP   0.013   0.001   TRP A1085 
 HIS   0.002   0.001   HIS A 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.23 (11609)
  covalent geometry    : angle       0.58931 /  0.39 (15945)
  hydrogen bonds       : bond        0.23263 / 23.73 (  548)
  hydrogen bonds       : angle       7.75211 /  8.13 ( 1522)
  Misc. bond           : bond        0.03681 /  1.84 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 181
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.8225 (tp) cc_final: 0.7962 (tp)
REVERT: A  536 GLN cc_start: 0.7593 (mt0) cc_final: 0.7258 (mt0)
REVERT: A  550 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7413 (mtpp)
REVERT: A  593 MET cc_start: 0.8428 (ttm) cc_final: 0.8195 (ttm)
REVERT: A  669 TYR cc_start: 0.6367 (t80) cc_final: 0.5972 (t80)
REVERT: A  816 THR cc_start: 0.7800 (p) cc_final: 0.7599 (p)
REVERT: A  893 ASN cc_start: 0.7664 (m-40) cc_final: 0.7341 (m-40)
REVERT: A 1021 ASP cc_start: 0.7181 (m-30) cc_final: 0.6911 (m-30)
REVERT: A 1087 THR cc_start: 0.7592 (p) cc_final: 0.7189 (m)
  outliers start: 12
  outliers final: 1
  residues processed: 193
  average time/residue: 0.1238
  time to fit residues: 32.6677
Evaluate side-chains
  160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:    0.0040
   chunk 103 optimal weight:    0.0470
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0770
   overall best weight:    0.2048

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 206 HIS
A 534 ASN
A1122 ASN
A1303 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.188159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.149728 restraints weight = 18827.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.150685 restraints weight = 9412.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.153743 restraints weight = 6690.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.153670 restraints weight = 5065.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.153679 restraints weight = 4421.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  11611  Z= 0.157
  Angle     :  0.610   9.359  15945  Z= 0.336
  Chirality :  0.042   0.199   1775
  Planarity :  0.005   0.037   1842
  Dihedral  : 18.720 175.096   2087
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.76 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.24), residues: 1232
  helix:  0.79 (0.21), residues: 595
  sheet: -0.36 (0.44), residues: 148
  loop : -0.08 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  43 
 TYR   0.049   0.002   TYR A  47 
 PHE   0.066   0.002   PHE A 162 
 TRP   0.008   0.001   TRP A1085 
 HIS   0.005   0.001   HIS A  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.16 (11609)
  covalent geometry    : angle       0.60984 /  0.34 (15945)
  hydrogen bonds       : bond        0.06240 /  6.37 (  548)
  hydrogen bonds       : angle       5.27788 /  5.36 ( 1522)
  Misc. bond           : bond        0.00851 /  0.43 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.6851 (m-30) cc_final: 0.6491 (m-30)
REVERT: A   50 LEU cc_start: 0.7788 (tp) cc_final: 0.7487 (tp)
REVERT: A  550 LYS cc_start: 0.7489 (mtpt) cc_final: 0.7259 (mtpp)
REVERT: A  593 MET cc_start: 0.8397 (ttm) cc_final: 0.8184 (ttm)
REVERT: A  981 ASP cc_start: 0.6866 (t0) cc_final: 0.6638 (t0)
REVERT: A 1021 ASP cc_start: 0.7019 (m-30) cc_final: 0.6711 (m-30)
REVERT: A 1252 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7341 (mtm180)
  outliers start: 11
  outliers final: 7
  residues processed: 169
  average time/residue: 0.1165
  time to fit residues: 26.8152
Evaluate side-chains
  167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  925 LYS
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1232 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 106 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0470
   chunk 29 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 534 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 872 HIS
A1122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.184506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.146055 restraints weight = 21045.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.146334 restraints weight = 10416.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147069 restraints weight = 8778.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.148139 restraints weight = 6507.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.148193 restraints weight = 5755.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11611  Z= 0.162
  Angle     :  0.566   8.003  15945  Z= 0.311
  Chirality :  0.043   0.241   1775
  Planarity :  0.005   0.077   1842
  Dihedral  : 18.686 175.115   2085
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.80 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1232
  helix:  1.26 (0.22), residues: 600
  sheet: -0.40 (0.44), residues: 148
  loop : -0.03 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1127 
 TYR   0.043   0.002   TYR A  47 
 PHE   0.067   0.002   PHE A 165 
 TRP   0.009   0.001   TRP A1085 
 HIS   0.005   0.001   HIS A1105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.16 (11609)
  covalent geometry    : angle       0.56590 /  0.31 (15945)
  hydrogen bonds       : bond        0.05148 /  5.14 (  548)
  hydrogen bonds       : angle       4.78924 /  4.87 ( 1522)
  Misc. bond           : bond        0.00321 /  0.16 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.6815 (m-30) cc_final: 0.6381 (m-30)
REVERT: A   50 LEU cc_start: 0.7888 (tp) cc_final: 0.7581 (tp)
REVERT: A  339 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6603 (tp)
REVERT: A  439 THR cc_start: 0.6701 (p) cc_final: 0.6474 (p)
REVERT: A  528 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7859 (t)
REVERT: A  550 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7274 (mtpp)
REVERT: A  593 MET cc_start: 0.8443 (ttm) cc_final: 0.8239 (ttp)
REVERT: A  786 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6615 (mt-10)
REVERT: A  893 ASN cc_start: 0.7775 (m-40) cc_final: 0.7522 (m-40)
REVERT: A  993 GLU cc_start: 0.7330 (pm20) cc_final: 0.7055 (pt0)
REVERT: A 1021 ASP cc_start: 0.6987 (m-30) cc_final: 0.6707 (m-30)
REVERT: A 1220 ARG cc_start: 0.5841 (mmm-85) cc_final: 0.5618 (tpp80)
REVERT: A 1250 ASP cc_start: 0.6436 (t0) cc_final: 0.6236 (t0)
  outliers start: 12
  outliers final: 4
  residues processed: 169
  average time/residue: 0.1246
  time to fit residues: 28.6166
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  925 LYS
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1232 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 96 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0060
   overall best weight:    0.6798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  12 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1105 HIS
A1122 ASN
A1296 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.184584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146220 restraints weight = 26715.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146355 restraints weight = 13189.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.147779 restraints weight = 8628.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148177 restraints weight = 6743.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.148273 restraints weight = 5949.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11611  Z= 0.164
  Angle     :  0.546   6.653  15945  Z= 0.299
  Chirality :  0.042   0.217   1775
  Planarity :  0.004   0.056   1842
  Dihedral  : 18.520 173.639   2085
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.90 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.25), residues: 1232
  helix:  1.44 (0.22), residues: 601
  sheet: -0.43 (0.44), residues: 148
  loop : -0.06 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1003 
 TYR   0.031   0.002   TYR A 173 
 PHE   0.033   0.002   PHE A1103 
 TRP   0.009   0.001   TRP A1085 
 HIS   0.004   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 (11609)
  covalent geometry    : angle       0.54554 /  0.30 (15945)
  hydrogen bonds       : bond        0.04306 /  4.30 (  548)
  hydrogen bonds       : angle       4.52358 /  4.58 ( 1522)
  Misc. bond           : bond        0.00225 /  0.11 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.6821 (m-30) cc_final: 0.6395 (m-30)
REVERT: A   50 LEU cc_start: 0.7947 (tp) cc_final: 0.7737 (tp)
REVERT: A  339 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6923 (tp)
REVERT: A  526 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5701 (m-80)
REVERT: A  529 GLU cc_start: 0.7561 (pm20) cc_final: 0.7353 (pm20)
REVERT: A  550 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7398 (mtpp)
REVERT: A  567 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7971 (mt)
REVERT: A  593 MET cc_start: 0.8539 (ttm) cc_final: 0.8313 (ttm)
REVERT: A  736 GLU cc_start: 0.7340 (tp30) cc_final: 0.7018 (tp30)
REVERT: A  786 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6541 (mt-10)
REVERT: A  806 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7167 (mtt)
REVERT: A  993 GLU cc_start: 0.7364 (pm20) cc_final: 0.7123 (pt0)
REVERT: A 1002 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7640 (ttmm)
REVERT: A 1021 ASP cc_start: 0.7001 (m-30) cc_final: 0.6721 (m-30)
REVERT: A 1115 LEU cc_start: 0.8139 (tp) cc_final: 0.7909 (tp)
REVERT: A 1118 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6693 (mttm)
REVERT: A 1250 ASP cc_start: 0.6446 (t0) cc_final: 0.6118 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 173
  average time/residue: 0.1139
  time to fit residues: 27.2839
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  925 LYS
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1257 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 111 optimal weight:    0.0170
   chunk 96 optimal weight:    0.7980
   chunk 102 optimal weight:    0.3980
   chunk 123 optimal weight:    0.2980
   chunk 61 optimal weight:    0.1980
   chunk 42 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.3218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
A1238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.185907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.145436 restraints weight = 17626.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148790 restraints weight = 8772.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.150543 restraints weight = 5582.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.151496 restraints weight = 4318.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.152317 restraints weight = 3874.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11611  Z= 0.116
  Angle     :  0.503   7.343  15945  Z= 0.277
  Chirality :  0.040   0.227   1775
  Planarity :  0.004   0.046   1842
  Dihedral  : 18.450 174.048   2085
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.09 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.25), residues: 1232
  helix:  1.67 (0.22), residues: 602
  sheet: -0.35 (0.44), residues: 148
  loop : -0.00 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1220 
 TYR   0.017   0.002   TYR A1106 
 PHE   0.032   0.001   PHE A 162 
 TRP   0.005   0.001   TRP A1085 
 HIS   0.004   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.12 (11609)
  covalent geometry    : angle       0.50301 /  0.28 (15945)
  hydrogen bonds       : bond        0.03833 /  3.77 (  548)
  hydrogen bonds       : angle       4.33203 /  4.38 ( 1522)
  Misc. bond           : bond        0.00079 /  0.04 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8024 (p)
REVERT: A   40 ASP cc_start: 0.7744 (m-30) cc_final: 0.7382 (m-30)
REVERT: A   45 ASP cc_start: 0.6834 (m-30) cc_final: 0.6413 (m-30)
REVERT: A   50 LEU cc_start: 0.7885 (tp) cc_final: 0.7629 (tp)
REVERT: A  235 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6693 (m)
REVERT: A  339 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6879 (tp)
REVERT: A  439 THR cc_start: 0.6953 (p) cc_final: 0.6710 (p)
REVERT: A  526 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5384 (m-80)
REVERT: A  528 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7896 (t)
REVERT: A  550 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7356 (mtpp)
REVERT: A  786 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6548 (mt-10)
REVERT: A  806 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7065 (mtt)
REVERT: A  993 GLU cc_start: 0.7271 (pm20) cc_final: 0.7068 (pt0)
REVERT: A 1002 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7617 (ttmt)
REVERT: A 1021 ASP cc_start: 0.6911 (m-30) cc_final: 0.6612 (m-30)
REVERT: A 1118 LYS cc_start: 0.7018 (mmtm) cc_final: 0.6679 (mttm)
REVERT: A 1238 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.6771 (t0)
REVERT: A 1250 ASP cc_start: 0.6403 (t0) cc_final: 0.6163 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 181
  average time/residue: 0.1158
  time to fit residues: 28.8652
Evaluate side-chains
  182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1238 ASN
Chi-restraints excluded: chain A residue 1257 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 123 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.184499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.144932 restraints weight = 19534.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.146131 restraints weight = 9549.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.147828 restraints weight = 7234.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.149457 restraints weight = 5090.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.149292 restraints weight = 4562.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11611  Z= 0.181
  Angle     :  0.534   7.058  15945  Z= 0.291
  Chirality :  0.042   0.229   1775
  Planarity :  0.004   0.049   1842
  Dihedral  : 18.500 173.350   2085
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.73 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.25), residues: 1232
  helix:  1.76 (0.22), residues: 602
  sheet: -0.53 (0.42), residues: 156
  loop :  0.06 (0.31), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1003 
 TYR   0.023   0.002   TYR A 595 
 PHE   0.035   0.002   PHE A1103 
 TRP   0.005   0.001   TRP A1298 
 HIS   0.004   0.001   HIS A  30 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.18 (11609)
  covalent geometry    : angle       0.53374 /  0.29 (15945)
  hydrogen bonds       : bond        0.03941 /  3.93 (  548)
  hydrogen bonds       : angle       4.29898 /  4.32 ( 1522)
  Misc. bond           : bond        0.00142 /  0.07 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8502 (p)
REVERT: A   40 ASP cc_start: 0.7746 (m-30) cc_final: 0.7495 (m-30)
REVERT: A   45 ASP cc_start: 0.6853 (m-30) cc_final: 0.6484 (m-30)
REVERT: A   50 LEU cc_start: 0.7761 (tp) cc_final: 0.7511 (tp)
REVERT: A  235 THR cc_start: 0.7142 (OUTLIER) cc_final: 0.6739 (m)
REVERT: A  339 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6929 (tp)
REVERT: A  526 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.5638 (m-80)
REVERT: A  528 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7861 (t)
REVERT: A  550 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7486 (mtpp)
REVERT: A  736 GLU cc_start: 0.7330 (tp30) cc_final: 0.6917 (tp30)
REVERT: A  786 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6634 (mt-10)
REVERT: A  806 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7167 (mtt)
REVERT: A  993 GLU cc_start: 0.7395 (pm20) cc_final: 0.7171 (pt0)
REVERT: A 1002 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7644 (ttmt)
REVERT: A 1021 ASP cc_start: 0.7109 (m-30) cc_final: 0.6811 (m-30)
REVERT: A 1118 LYS cc_start: 0.7077 (mmtm) cc_final: 0.6714 (mttm)
  outliers start: 19
  outliers final: 9
  residues processed: 175
  average time/residue: 0.1109
  time to fit residues: 26.8401
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1244 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 95 optimal weight:    0.0670
   chunk 111 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 126 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0670
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0050
   overall best weight:    0.3470

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 GLN
A1122 ASN
A1238 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.185897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.147016 restraints weight = 25017.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.148468 restraints weight = 11706.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.149167 restraints weight = 8628.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149806 restraints weight = 6794.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.149820 restraints weight = 5814.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11611  Z= 0.117
  Angle     :  0.508   6.922  15945  Z= 0.277
  Chirality :  0.040   0.236   1775
  Planarity :  0.004   0.040   1842
  Dihedral  : 18.447 173.572   2085
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.19 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.25), residues: 1232
  helix:  1.90 (0.22), residues: 603
  sheet: -0.56 (0.42), residues: 156
  loop :  0.05 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1003 
 TYR   0.017   0.001   TYR A 168 
 PHE   0.035   0.001   PHE A1103 
 TRP   0.005   0.001   TRP A 676 
 HIS   0.004   0.000   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.12 (11609)
  covalent geometry    : angle       0.50794 /  0.28 (15945)
  hydrogen bonds       : bond        0.03575 /  3.54 (  548)
  hydrogen bonds       : angle       4.19212 /  4.20 ( 1522)
  Misc. bond           : bond        0.00088 /  0.04 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (p)
REVERT: A   40 ASP cc_start: 0.7670 (m-30) cc_final: 0.7454 (m-30)
REVERT: A   45 ASP cc_start: 0.6779 (m-30) cc_final: 0.6453 (m-30)
REVERT: A   50 LEU cc_start: 0.7917 (tp) cc_final: 0.7673 (tp)
REVERT: A  235 THR cc_start: 0.7169 (OUTLIER) cc_final: 0.6728 (m)
REVERT: A  339 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6931 (tp)
REVERT: A  526 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5539 (m-80)
REVERT: A  528 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7950 (t)
REVERT: A  550 LYS cc_start: 0.7532 (mtpt) cc_final: 0.7308 (mtpp)
REVERT: A  567 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7957 (mt)
REVERT: A  736 GLU cc_start: 0.7291 (tp30) cc_final: 0.6899 (tp30)
REVERT: A  806 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7091 (mtt)
REVERT: A  993 GLU cc_start: 0.7308 (pm20) cc_final: 0.7084 (pt0)
REVERT: A 1002 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7626 (ttmt)
REVERT: A 1021 ASP cc_start: 0.6969 (m-30) cc_final: 0.6672 (m-30)
REVERT: A 1118 LYS cc_start: 0.7012 (mmtm) cc_final: 0.6650 (mttm)
REVERT: A 1238 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.6743 (t0)
REVERT: A 1250 ASP cc_start: 0.6416 (t0) cc_final: 0.6133 (t0)
  outliers start: 26
  outliers final: 12
  residues processed: 180
  average time/residue: 0.1018
  time to fit residues: 25.7615
Evaluate side-chains
  186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1170 THR
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1238 ASN
Chi-restraints excluded: chain A residue 1244 LEU
Chi-restraints excluded: chain A residue 1257 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 120 optimal weight:    0.3980
   chunk 122 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0370
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0870
   overall best weight:    0.3636

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.185146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.145713 restraints weight = 16563.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.147573 restraints weight = 9587.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.150626 restraints weight = 6211.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.150735 restraints weight = 4792.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.150797 restraints weight = 4006.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11611  Z= 0.119
  Angle     :  0.516   8.081  15945  Z= 0.281
  Chirality :  0.041   0.240   1775
  Planarity :  0.004   0.036   1842
  Dihedral  : 18.411 173.595   2085
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.65 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.25), residues: 1232
  helix:  1.89 (0.22), residues: 603
  sheet: -0.54 (0.42), residues: 156
  loop :  0.06 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1003 
 TYR   0.017   0.001   TYR A 168 
 PHE   0.038   0.001   PHE A1103 
 TRP   0.010   0.001   TRP A 483 
 HIS   0.003   0.000   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 (11609)
  covalent geometry    : angle       0.51613 /  0.28 (15945)
  hydrogen bonds       : bond        0.03588 /  3.58 (  548)
  hydrogen bonds       : angle       4.17926 /  4.22 ( 1522)
  Misc. bond           : bond        0.00087 /  0.04 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8510 (p)
REVERT: A   40 ASP cc_start: 0.7641 (m-30) cc_final: 0.7414 (m-30)
REVERT: A   45 ASP cc_start: 0.6796 (m-30) cc_final: 0.6485 (m-30)
REVERT: A   50 LEU cc_start: 0.7793 (tp) cc_final: 0.7504 (tp)
REVERT: A  235 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6694 (m)
REVERT: A  339 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6905 (tp)
REVERT: A  526 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.5482 (m-80)
REVERT: A  550 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7292 (mtpp)
REVERT: A  567 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7966 (mt)
REVERT: A  736 GLU cc_start: 0.7185 (tp30) cc_final: 0.6844 (tp30)
REVERT: A  806 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7131 (mtt)
REVERT: A  993 GLU cc_start: 0.7280 (pm20) cc_final: 0.7077 (pt0)
REVERT: A 1002 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7620 (ttmt)
REVERT: A 1021 ASP cc_start: 0.6929 (m-30) cc_final: 0.6632 (m-30)
REVERT: A 1118 LYS cc_start: 0.6982 (mmtm) cc_final: 0.6629 (mttm)
  outliers start: 24
  outliers final: 12
  residues processed: 176
  average time/residue: 0.1290
  time to fit residues: 31.6019
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  952 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1170 THR
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1244 LEU
Chi-restraints excluded: chain A residue 1257 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0980
   chunk 71 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0970
   chunk 26 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  70 GLN
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.184847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.144500 restraints weight = 18625.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.146678 restraints weight = 9480.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.149013 restraints weight = 6156.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.150121 restraints weight = 4562.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.151116 restraints weight = 3932.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3813 r_free = 0.3813    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3813 r_free = 0.3813    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11611  Z= 0.132
  Angle     :  0.529   7.831  15945  Z= 0.287
  Chirality :  0.041   0.243   1775
  Planarity :  0.004   0.035   1842
  Dihedral  : 18.366 173.336   2085
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.39 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.25), residues: 1232
  helix:  1.88 (0.21), residues: 608
  sheet: -0.54 (0.42), residues: 156
  loop :  0.11 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 833 
 TYR   0.019   0.002   TYR A 168 
 PHE   0.042   0.002   PHE A 165 
 TRP   0.004   0.001   TRP A 676 
 HIS   0.003   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 (11609)
  covalent geometry    : angle       0.52938 /  0.29 (15945)
  hydrogen bonds       : bond        0.03582 /  3.61 (  548)
  hydrogen bonds       : angle       4.15904 /  4.21 ( 1522)
  Misc. bond           : bond        0.00105 /  0.05 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8506 (p)
REVERT: A   40 ASP cc_start: 0.7618 (m-30) cc_final: 0.7363 (m-30)
REVERT: A   45 ASP cc_start: 0.6749 (m-30) cc_final: 0.6465 (m-30)
REVERT: A   50 LEU cc_start: 0.7873 (tp) cc_final: 0.7583 (tp)
REVERT: A  235 THR cc_start: 0.7101 (OUTLIER) cc_final: 0.6661 (m)
REVERT: A  339 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6953 (tp)
REVERT: A  526 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5458 (m-80)
REVERT: A  550 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7312 (mtpp)
REVERT: A  567 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7977 (mt)
REVERT: A  736 GLU cc_start: 0.7158 (tp30) cc_final: 0.6751 (tp30)
REVERT: A  806 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7127 (mtt)
REVERT: A 1002 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7613 (ttmt)
REVERT: A 1021 ASP cc_start: 0.6938 (m-30) cc_final: 0.6644 (m-30)
REVERT: A 1087 THR cc_start: 0.7710 (p) cc_final: 0.7348 (m)
REVERT: A 1118 LYS cc_start: 0.6983 (mmtm) cc_final: 0.6617 (mttm)
REVERT: A 1238 ASN cc_start: 0.8053 (t0) cc_final: 0.7254 (t0)
REVERT: A 1250 ASP cc_start: 0.6450 (t0) cc_final: 0.6093 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 174
  average time/residue: 0.1195
  time to fit residues: 29.1802
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  952 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1170 THR
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1244 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 50 optimal weight:    0.2980
   chunk 77 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0050
   chunk 45 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  70 GLN
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.185079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147037 restraints weight = 16873.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.148245 restraints weight = 9507.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.149478 restraints weight = 6260.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.149755 restraints weight = 5343.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149962 restraints weight = 5046.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11611  Z= 0.125
  Angle     :  0.526   7.357  15945  Z= 0.285
  Chirality :  0.041   0.243   1775
  Planarity :  0.004   0.037   1842
  Dihedral  : 18.322 173.275   2085
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.58 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.25), residues: 1232
  helix:  1.88 (0.21), residues: 610
  sheet: -0.53 (0.42), residues: 156
  loop :  0.12 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 833 
 TYR   0.022   0.001   TYR A 168 
 PHE   0.032   0.001   PHE A 165 
 TRP   0.004   0.001   TRP A 676 
 HIS   0.013   0.001   HIS A1105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 (11609)
  covalent geometry    : angle       0.52602 /  0.29 (15945)
  hydrogen bonds       : bond        0.03517 /  3.54 (  548)
  hydrogen bonds       : angle       4.14492 /  4.19 ( 1522)
  Misc. bond           : bond        0.00091 /  0.05 (    2)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8444 (p)
REVERT: A   40 ASP cc_start: 0.7630 (m-30) cc_final: 0.7401 (m-30)
REVERT: A   50 LEU cc_start: 0.7816 (tp) cc_final: 0.7558 (tp)
REVERT: A  235 THR cc_start: 0.7110 (OUTLIER) cc_final: 0.6667 (m)
REVERT: A  339 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6947 (tp)
REVERT: A  526 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.5463 (m-80)
REVERT: A  550 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7418 (mtpp)
REVERT: A  567 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7927 (mt)
REVERT: A  622 HIS cc_start: 0.5089 (t70) cc_final: 0.4660 (t-170)
REVERT: A  736 GLU cc_start: 0.7295 (tp30) cc_final: 0.6902 (tp30)
REVERT: A  806 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7105 (mtt)
REVERT: A 1002 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7633 (ttmt)
REVERT: A 1021 ASP cc_start: 0.7070 (m-30) cc_final: 0.6759 (m-30)
REVERT: A 1087 THR cc_start: 0.7700 (p) cc_final: 0.7386 (m)
REVERT: A 1118 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6648 (mttm)
REVERT: A 1238 ASN cc_start: 0.8110 (t0) cc_final: 0.7363 (t0)
REVERT: A 1250 ASP cc_start: 0.6507 (t0) cc_final: 0.6206 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 173
  average time/residue: 0.1231
  time to fit residues: 29.7028
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  952 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 HIS
Chi-restraints excluded: chain A residue 1170 THR
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1244 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 79 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  70 GLN
** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
** A1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.184807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.146594 restraints weight = 16618.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.148139 restraints weight = 9590.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.149408 restraints weight = 6363.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149472 restraints weight = 5304.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.149858 restraints weight = 5142.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115  11611  Z= 0.184
  Angle     :  0.815  59.194  15945  Z= 0.473
  Chirality :  0.041   0.243   1775
  Planarity :  0.004   0.034   1842
  Dihedral  : 18.320 173.227   2085
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.39 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.25), residues: 1232
  helix:  1.87 (0.21), residues: 610
  sheet: -0.56 (0.42), residues: 156
  loop :  0.11 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A  43 
 TYR   0.022   0.002   TYR A 168 
 PHE   0.032   0.002   PHE A 162 
 TRP   0.014   0.001   TRP A1085 
 HIS   0.016   0.001   HIS A1105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.18 (11609)
  covalent geometry    : angle       0.81543 /  0.47 (15945)
  hydrogen bonds       : bond        0.03532 /  3.56 (  548)
  hydrogen bonds       : angle       4.14325 /  4.19 ( 1522)
  Misc. bond           : bond        0.00143 /  0.07 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2102.14 seconds
wall clock time: 36 minutes 54.52 seconds (2214.52 seconds total)