Starting phenix.real_space_refine
on Sat Jul  4 05:49:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cjh_45631/07_2026/9cjh_45631.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cjh_45631/07_2026/9cjh_45631.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cjh_45631/07_2026/9cjh_45631.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cjh_45631/07_2026/9cjh_45631.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cjh_45631/07_2026/9cjh_45631.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cjh_45631/07_2026/9cjh_45631.cif"
  }
  resolution = 3.6
  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 9382 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    6976      2.51       5
     N    1910      2.21       5
     O    2230      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11200
  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: 10013
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1236, 10013
          Classifications: {'peptide': 1236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 47, 'TRANS': 1188}
          Chain breaks: 4
          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: 127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 127
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    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: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 328
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 2.76, per 1000 atoms: 0.25
  Number of scatterers: 11200
  At special positions: 0
  Unit cell: (98.12, 107.04, 139.375, 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    2230      8.00
     N    1910      7.00
     C    6976      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 481.3 milliseconds
  

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 12 sheets defined
      55.0% alpha, 10.8% beta
      16 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 1.30
  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 45
    Processing helix  chain 'A' and resid 49 through 68
      removed outlier: 4.248A  pdb=" N   ILE A  53 " --> pdb=" O   GLU A  49 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ILE A  57 " --> pdb=" O   ILE A  53 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR A  58 " --> pdb=" O   ILE A  54 " (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: 3.751A  pdb=" N   ALA A 126 " --> pdb=" O   ASN A 122 " (cutoff:3.500A)
      removed outlier: 3.572A  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: 3.786A  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: 4.069A  pdb=" N   VAL A 329 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE A 330 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG A 341 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 3.627A  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: 3.728A  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: 3.658A  pdb=" N   ILE A 466 " --> pdb=" O   GLU A 462 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP A 482 " --> pdb=" O   TYR A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
    Processing helix  chain 'A' and resid 508 through 523
      removed outlier: 4.308A  pdb=" N   SER A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 600 through 609
      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
    Processing helix  chain 'A' and resid 657 through 662
    Processing helix  chain 'A' and resid 665 through 687
    Processing helix  chain 'A' and resid 694 through 698
      removed outlier: 3.713A  pdb=" N   SER A 697 " --> pdb=" O   ASP A 694 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 698 " --> pdb=" O   LEU A 695 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 694 through 698'
    Processing helix  chain 'A' and resid 706 through 719
      removed outlier: 3.635A  pdb=" N   TYR A 710 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      Proline residue:  A 716  - end of helix
      removed outlier: 3.895A  pdb=" N   TYR A 719 " --> pdb=" O   ASN A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 737
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.622A  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
    Processing helix  chain 'A' and resid 839 through 846
    Processing helix  chain 'A' and resid 847 through 849
      No H-bonds generated for 'chain 'A' and resid 847 through 849'
    Processing helix  chain 'A' and resid 861 through 865
      removed outlier: 3.785A  pdb=" N   PHE A 864 " --> pdb=" O   ASP A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 899
    Processing helix  chain 'A' and resid 943 through 955
    Processing helix  chain 'A' and resid 958 through 987
      removed outlier: 3.709A  pdb=" N   HIS A 977 " --> pdb=" O   SER A 973 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU A 978 " --> pdb=" O   GLN A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1025
      removed outlier: 3.509A  pdb=" N   LYS A1017 " --> pdb=" O   GLN A1013 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   CYS A1025 " --> pdb=" O   ASP A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1101
      removed outlier: 4.046A  pdb=" N   PHE A1101 " --> pdb=" O   PHE A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1190
    Processing helix  chain 'A' and resid 1199 through 1207
    Processing helix  chain 'A' and resid 1208 through 1224
      removed outlier: 3.533A  pdb=" N   VAL A1216 " --> pdb=" O   ILE A1212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1261 through 1284
      removed outlier: 3.520A  pdb=" N   GLY A1266 " --> pdb=" O   ALA A1262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1307
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532
      removed outlier: 4.158A  pdb=" N   PHE A 869 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR A 563 " --> pdb=" O   ILE A 745 " (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 589 through 596
    Processing sheet with id=AA5, first strand: chain 'A' and resid 626 through 628
    Processing sheet with id=AA6, first strand: chain 'A' and resid 799 through 800
      removed outlier: 3.594A  pdb=" N   ILE A 858 " --> pdb=" O   HIS A 800 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 807
    Processing sheet with id=AA8, first strand: chain 'A' and resid 926 through 931
      removed outlier: 6.750A  pdb=" N   VAL A 919 " --> pdb=" O   LEU A 927 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLN A 929 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE A 917 " --> pdb=" O   GLN A 929 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE A 905 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   GLU A 993 " --> pdb=" O   ILE A 905 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   ILE A 907 " --> pdb=" O   GLU A 993 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1103 through 1107
      removed outlier: 3.993A  pdb=" N   PHE A1103 " --> pdb=" O   HIS A1116 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP A1112 " --> pdb=" O   ASP A1107 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1145 through 1147
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1159 through 1161
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1226 through 1229

    509 hydrogen bonds defined for protein.
    1431 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 1.46 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: 2191
        1.33 -     1.45: 3034
        1.45 -     1.57: 6186
        1.57 -     1.69: 111
        1.69 -     1.81: 44
  Bond restraints: 11566
  Sorted by residual:
  bond pdb=" O5' 2YR C   7 "
       pdb=" P   2YR C   7 "
    ideal  model  delta    sigma   weight residual
    1.721  1.599  0.122 2.00e-02 2.50e+03 3.73e+01
  bond pdb=" N   ILE A 626 "
       pdb=" CA  ILE A 626 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.29e-02 6.01e+03 9.99e+00
  bond pdb=" CB  PRO A 700 "
       pdb=" CG  PRO A 700 "
    ideal  model  delta    sigma   weight residual
    1.492  1.643 -0.151 5.00e-02 4.00e+02 9.07e+00
  bond pdb=" C3'  DC D  21 "
       pdb=" C2'  DC D  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.46e+00
  bond pdb=" C3'  DA D  22 "
       pdb=" C2'  DA D  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.02e+00
  ... (remaining 11561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 15740
        2.53 -     5.06: 136
        5.06 -     7.59: 7
        7.59 -    10.12: 2
       10.12 -    12.65: 1
  Bond angle restraints: 15886
  Sorted by residual:
  angle pdb=" CA  PRO A 700 "
        pdb=" N   PRO A 700 "
        pdb=" CD  PRO A 700 "
      ideal   model   delta    sigma   weight residual
     112.00   99.35   12.65 1.40e+00 5.10e-01 8.16e+01
  angle pdb=" N   HIS A  46 "
        pdb=" CA  HIS A  46 "
        pdb=" C   HIS A  46 "
      ideal   model   delta    sigma   weight residual
     113.50  104.52    8.98 1.23e+00 6.61e-01 5.33e+01
  angle pdb=" O   GLU A 634 "
        pdb=" C   GLU A 634 "
        pdb=" N   PRO A 635 "
      ideal   model   delta    sigma   weight residual
     121.80  117.60    4.20 8.60e-01 1.35e+00 2.39e+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  122.61   -2.71 6.00e-01 2.78e+00 2.04e+01
  angle pdb=" O4   DT C  10 "
        pdb=" C4   DT C  10 "
        pdb=" C5   DT C  10 "
      ideal   model   delta    sigma   weight residual
     124.90  121.92    2.98 7.00e-01 2.04e+00 1.82e+01
  ... (remaining 15881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.55: 6510
       33.55 -    67.10: 356
       67.10 -   100.65: 32
      100.65 -   134.20: 1
      134.20 -   167.75: 2
  Dihedral angle restraints: 6901
    sinusoidal: 3251
      harmonic: 3650
  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   64.25  167.75     1      1.70e+01 3.46e-03 6.57e+01
  dihedral pdb=" C4'  DA D  24 "
           pdb=" C3'  DA D  24 "
           pdb=" O3'  DA D  24 "
           pdb=" P    DG D  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   61.57  158.43     1      3.50e+01 8.16e-04 1.51e+01
  dihedral pdb=" CA  PHE A 598 "
           pdb=" C   PHE A 598 "
           pdb=" N   PRO A 599 "
           pdb=" CA  PRO A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.28  -18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 6898 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1515
       0.055 -    0.110: 225
       0.110 -    0.166: 27
       0.166 -    0.221: 4
       0.221 -    0.276: 1
  Chirality restraints: 1772
  Sorted by residual:
  chirality pdb=" CA  LEU A 636 "
            pdb=" N   LEU A 636 "
            pdb=" C   LEU A 636 "
            pdb=" CB  LEU A 636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.90e+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    2.47   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  LEU A 627 "
            pdb=" N   LEU A 627 "
            pdb=" C   LEU A 627 "
            pdb=" CB  LEU A 627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.65e-01
  ... (remaining 1769 not shown)

  Planarity restraints: 1836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' 2YR C   7 "   -0.243 2.00e-02 2.50e+03   3.00e-01 2.24e+03
        pdb=" C2  2YR C   7 "    0.014 2.00e-02 2.50e+03
        pdb=" C4  2YR C   7 "    0.261 2.00e-02 2.50e+03
        pdb=" C5  2YR C   7 "    0.185 2.00e-02 2.50e+03
        pdb=" C6  2YR C   7 "    0.026 2.00e-02 2.50e+03
        pdb=" C9  2YR C   7 "   -0.719 2.00e-02 2.50e+03
        pdb=" N1  2YR C   7 "   -0.059 2.00e-02 2.50e+03
        pdb=" N3  2YR C   7 "    0.178 2.00e-02 2.50e+03
        pdb=" N4  2YR C   7 "    0.423 2.00e-02 2.50e+03
        pdb=" O2  2YR C   7 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 699 "    0.095 5.00e-02 4.00e+02   1.35e-01 2.93e+01
        pdb=" N   PRO A 700 "   -0.234 5.00e-02 4.00e+02
        pdb=" CA  PRO A 700 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO A 700 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 624 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.27e+00
        pdb=" C   THR A 624 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR A 624 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PRO A 625 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1833 not shown)

  Histogram of nonbonded interaction distances:
        1.27 -     2.00: 8
        2.00 -     2.72: 465
        2.72 -     3.45: 16203
        3.45 -     4.17: 27475
        4.17 -     4.90: 48166
  Nonbonded interactions: 92317
  Sorted by model distance:
  nonbonded pdb=" CB  LYS A 164 "
            pdb=" CG  PRO A 538 "
     model   vdw
     1.271 3.840
  nonbonded pdb=" CE2 PHE A 165 "
            pdb=" OD1 ASN A 534 "
     model   vdw
     1.637 2.672
  nonbonded pdb=" CZ  PHE A 165 "
            pdb=" OD1 ASN A 534 "
     model   vdw
     1.694 3.340
  nonbonded pdb=" CD  ARG A  43 "
            pdb=" O   SER A 161 "
     model   vdw
     1.702 3.440
  nonbonded pdb=" NE  ARG A  43 "
            pdb=" O   SER A 161 "
     model   vdw
     1.751 3.120
  ... (remaining 92312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.470
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
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      :  0.004   0.228  11569  Z= 0.324
  Angle     :  0.599  12.649  15886  Z= 0.405
  Chirality :  0.041   0.276   1772
  Planarity :  0.008   0.300   1836
  Dihedral  : 18.328 167.752   4537
  Min Nonbonded Distance : 1.271

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  2.50 %
    Favored  : 96.67 %
  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: -0.88 (0.23), residues: 1226
  helix: -0.46 (0.20), residues: 591
  sheet: -0.75 (0.45), residues: 134
  loop : -0.45 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1121 
 TYR   0.013   0.001   TYR A 526 
 PHE   0.015   0.001   PHE A1132 
 TRP   0.009   0.001   TRP A 958 
 HIS   0.002   0.001   HIS A  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.24 (11566)
  covalent geometry    : angle       0.59917 /  0.40 (15886)
  hydrogen bonds       : bond        0.23019 / 22.61 (  539)
  hydrogen bonds       : angle       7.54779 /  7.31 ( 1507)
  Misc. bond           : bond        0.13485 /  6.85 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 191
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 TYR cc_start: 0.7846 (p90) cc_final: 0.7499 (p90)
REVERT: A   34 GLN cc_start: 0.6867 (tp-100) cc_final: 0.6578 (tm-30)
REVERT: A  471 LEU cc_start: 0.6945 (mt) cc_final: 0.6729 (mt)
REVERT: A  558 VAL cc_start: 0.8422 (p) cc_final: 0.8086 (p)
REVERT: A  583 THR cc_start: 0.8415 (p) cc_final: 0.8155 (t)
REVERT: A  604 MET cc_start: 0.6809 (mmp) cc_final: 0.5536 (mmt)
REVERT: A  720 HIS cc_start: 0.7197 (t-90) cc_final: 0.6885 (t-170)
REVERT: A  860 LYS cc_start: 0.8126 (tmmt) cc_final: 0.7739 (tmmt)
REVERT: A  937 GLN cc_start: 0.7219 (tp-100) cc_final: 0.6958 (tp-100)
REVERT: A  949 LYS cc_start: 0.6963 (tptp) cc_final: 0.6580 (tptp)
REVERT: A 1021 ASP cc_start: 0.6997 (m-30) cc_final: 0.6774 (m-30)
REVERT: A 1191 ILE cc_start: 0.7994 (mm) cc_final: 0.7787 (mt)
REVERT: A 1199 ILE cc_start: 0.8277 (mm) cc_final: 0.7946 (mm)
REVERT: A 1215 MET cc_start: 0.7800 (tpt) cc_final: 0.7549 (tpt)
REVERT: A 1242 ARG cc_start: 0.6721 (ptp-110) cc_final: 0.6451 (ptp-110)
  outliers start: 9
  outliers final: 2
  residues processed: 200
  average time/residue: 0.1236
  time to fit residues: 33.7597
Evaluate side-chains
  179 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 177
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  346 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0370
   chunk 123 optimal weight:    0.0060
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.3674

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 HIS
A 666 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 ASN
A1013 GLN
A1091 HIS
A1229 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.191367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150907 restraints weight = 17143.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151353 restraints weight = 10356.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153501 restraints weight = 6731.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153497 restraints weight = 5338.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.153713 restraints weight = 4887.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11569  Z= 0.152
  Angle     :  0.609  10.312  15886  Z= 0.325
  Chirality :  0.042   0.303   1772
  Planarity :  0.005   0.066   1836
  Dihedral  : 18.910 169.071   2076
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.06 %
    Favored  : 89.93 %
  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:  0.32 (0.24), residues: 1226
  helix:  0.97 (0.21), residues: 610
  sheet: -1.03 (0.44), residues: 122
  loop : -0.29 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  43 
 TYR   0.024   0.002   TYR A 687 
 PHE   0.023   0.001   PHE A 165 
 TRP   0.010   0.001   TRP A 958 
 HIS   0.005   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.15 (11566)
  covalent geometry    : angle       0.60892 /  0.33 (15886)
  hydrogen bonds       : bond        0.05474 /  5.36 (  539)
  hydrogen bonds       : angle       4.90754 /  4.74 ( 1507)
  Misc. bond           : bond        0.01216 /  0.61 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.6919 (tp-100) cc_final: 0.6500 (tm-30)
REVERT: A  583 THR cc_start: 0.8448 (p) cc_final: 0.8214 (t)
REVERT: A  720 HIS cc_start: 0.7033 (t-90) cc_final: 0.6757 (t-170)
REVERT: A  805 LYS cc_start: 0.7506 (mmtm) cc_final: 0.7261 (mmtp)
REVERT: A  841 GLU cc_start: 0.7035 (pm20) cc_final: 0.6592 (pm20)
REVERT: A  860 LYS cc_start: 0.8223 (tmmt) cc_final: 0.7791 (tmmt)
REVERT: A  937 GLN cc_start: 0.7248 (tp-100) cc_final: 0.7048 (tp-100)
REVERT: A  949 LYS cc_start: 0.6811 (tptp) cc_final: 0.6387 (tptp)
REVERT: A  963 THR cc_start: 0.7918 (p) cc_final: 0.7627 (t)
REVERT: A  971 TYR cc_start: 0.7738 (t80) cc_final: 0.7445 (t80)
REVERT: A 1021 ASP cc_start: 0.7023 (m-30) cc_final: 0.6759 (m-30)
REVERT: A 1099 GLU cc_start: 0.7014 (tp30) cc_final: 0.6792 (tp30)
REVERT: A 1191 ILE cc_start: 0.7959 (mm) cc_final: 0.7717 (mt)
REVERT: A 1199 ILE cc_start: 0.8275 (mm) cc_final: 0.7936 (mm)
REVERT: A 1242 ARG cc_start: 0.6770 (ptp-110) cc_final: 0.6565 (ptp-110)
REVERT: A 1260 MET cc_start: 0.7618 (mmt) cc_final: 0.7266 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 182
  average time/residue: 0.1238
  time to fit residues: 30.3928
Evaluate side-chains
  175 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 168
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  969 GLN
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0980
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.189753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.146486 restraints weight = 17055.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149928 restraints weight = 8214.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.151687 restraints weight = 5239.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.153076 restraints weight = 4150.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153747 restraints weight = 3619.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11569  Z= 0.156
  Angle     :  0.562   7.035  15886  Z= 0.301
  Chirality :  0.042   0.301   1772
  Planarity :  0.004   0.052   1836
  Dihedral  : 18.814 168.587   2073
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.37 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.68 (0.24), residues: 1226
  helix:  1.44 (0.21), residues: 611
  sheet: -0.86 (0.43), residues: 137
  loop : -0.34 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 862 
 TYR   0.020   0.002   TYR A 595 
 PHE   0.011   0.001   PHE A 531 
 TRP   0.012   0.001   TRP A 676 
 HIS   0.004   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.16 (11566)
  covalent geometry    : angle       0.56185 /  0.30 (15886)
  hydrogen bonds       : bond        0.04304 /  4.23 (  539)
  hydrogen bonds       : angle       4.44381 /  4.30 ( 1507)
  Misc. bond           : bond        0.00426 /  0.21 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7321 (tp30) cc_final: 0.6961 (tp30)
REVERT: A   34 GLN cc_start: 0.7007 (tp-100) cc_final: 0.6521 (tm-30)
REVERT: A  516 LYS cc_start: 0.6568 (tttt) cc_final: 0.6367 (tttt)
REVERT: A  583 THR cc_start: 0.8411 (p) cc_final: 0.8183 (t)
REVERT: A  720 HIS cc_start: 0.7123 (t-90) cc_final: 0.6822 (t70)
REVERT: A  776 LYS cc_start: 0.7722 (pptt) cc_final: 0.7446 (pptt)
REVERT: A  841 GLU cc_start: 0.7089 (pm20) cc_final: 0.6751 (pm20)
REVERT: A  860 LYS cc_start: 0.8215 (tmmt) cc_final: 0.7763 (tmmt)
REVERT: A  861 ASP cc_start: 0.7301 (m-30) cc_final: 0.7033 (m-30)
REVERT: A  949 LYS cc_start: 0.6820 (tptp) cc_final: 0.6347 (tptp)
REVERT: A  971 TYR cc_start: 0.7678 (t80) cc_final: 0.7289 (t80)
REVERT: A 1021 ASP cc_start: 0.7099 (m-30) cc_final: 0.6801 (m-30)
REVERT: A 1099 GLU cc_start: 0.7097 (tp30) cc_final: 0.6832 (tp30)
REVERT: A 1191 ILE cc_start: 0.7942 (mm) cc_final: 0.7737 (mt)
REVERT: A 1199 ILE cc_start: 0.8226 (mm) cc_final: 0.7944 (mm)
REVERT: A 1215 MET cc_start: 0.7999 (tpp) cc_final: 0.7783 (tpt)
REVERT: A 1242 ARG cc_start: 0.6860 (ptp-110) cc_final: 0.6574 (ptp-110)
  outliers start: 13
  outliers final: 9
  residues processed: 174
  average time/residue: 0.1406
  time to fit residues: 32.8691
Evaluate side-chains
  176 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 167
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1155 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0870
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 145 GLN
A 647 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 ASN
A1044 GLN
A1091 HIS
A1105 HIS
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.188543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144784 restraints weight = 17198.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.148246 restraints weight = 8322.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150365 restraints weight = 5324.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151296 restraints weight = 4153.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.151974 restraints weight = 3700.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11569  Z= 0.154
  Angle     :  0.555  10.658  15886  Z= 0.295
  Chirality :  0.042   0.297   1772
  Planarity :  0.004   0.046   1836
  Dihedral  : 18.817 168.533   2073
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.20 %
    Favored  : 85.67 %
  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:  0.82 (0.24), residues: 1226
  helix:  1.65 (0.22), residues: 611
  sheet: -0.89 (0.42), residues: 135
  loop : -0.39 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 725 
 TYR   0.020   0.001   TYR A 595 
 PHE   0.025   0.001   PHE A1103 
 TRP   0.009   0.001   TRP A 676 
 HIS   0.004   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 (11566)
  covalent geometry    : angle       0.55497 /  0.29 (15886)
  hydrogen bonds       : bond        0.03809 /  3.77 (  539)
  hydrogen bonds       : angle       4.21008 /  4.05 ( 1507)
  Misc. bond           : bond        0.00246 /  0.12 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6570 (tm-30)
REVERT: A  537 MET cc_start: 0.7916 (mtp) cc_final: 0.7655 (mtp)
REVERT: A  568 MET cc_start: 0.7884 (mpp) cc_final: 0.7220 (mtp)
REVERT: A  583 THR cc_start: 0.8418 (p) cc_final: 0.8200 (t)
REVERT: A  720 HIS cc_start: 0.7132 (t-90) cc_final: 0.6810 (t70)
REVERT: A  841 GLU cc_start: 0.7090 (pm20) cc_final: 0.6843 (pm20)
REVERT: A  860 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7823 (tmmt)
REVERT: A  861 ASP cc_start: 0.7385 (m-30) cc_final: 0.7096 (m-30)
REVERT: A  949 LYS cc_start: 0.6839 (tptp) cc_final: 0.6311 (tptp)
REVERT: A  951 ARG cc_start: 0.5762 (ttt180) cc_final: 0.5519 (ttt180)
REVERT: A  971 TYR cc_start: 0.7647 (t80) cc_final: 0.7212 (t80)
REVERT: A 1021 ASP cc_start: 0.7067 (m-30) cc_final: 0.6760 (m-30)
REVERT: A 1081 ASP cc_start: 0.7474 (t0) cc_final: 0.7270 (t0)
REVERT: A 1099 GLU cc_start: 0.7107 (tp30) cc_final: 0.6788 (tp30)
REVERT: A 1199 ILE cc_start: 0.8197 (mm) cc_final: 0.7899 (mm)
REVERT: A 1215 MET cc_start: 0.8020 (tpp) cc_final: 0.7770 (tpt)
REVERT: A 1242 ARG cc_start: 0.6860 (ptp-110) cc_final: 0.6596 (ptp-110)
  outliers start: 23
  outliers final: 16
  residues processed: 177
  average time/residue: 0.1340
  time to fit residues: 32.2658
Evaluate side-chains
  178 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue 1001 SER
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1124 SER
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1155 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0070
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7600

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 ASN
A 647 ASN
A1091 HIS
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.188000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.145008 restraints weight = 16930.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.148422 restraints weight = 8145.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150580 restraints weight = 5207.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.151613 restraints weight = 4023.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152325 restraints weight = 3536.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11569  Z= 0.168
  Angle     :  0.561   8.474  15886  Z= 0.298
  Chirality :  0.042   0.296   1772
  Planarity :  0.004   0.065   1836
  Dihedral  : 18.843 168.589   2073
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.59 %
    Favored  : 84.47 %
  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:  0.95 (0.25), residues: 1226
  helix:  1.75 (0.22), residues: 614
  sheet: -0.93 (0.41), residues: 135
  loop : -0.30 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 947 
 TYR   0.022   0.002   TYR A 595 
 PHE   0.025   0.001   PHE A1103 
 TRP   0.009   0.001   TRP A 676 
 HIS   0.005   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 (11566)
  covalent geometry    : angle       0.56143 /  0.30 (15886)
  hydrogen bonds       : bond        0.03733 /  3.69 (  539)
  hydrogen bonds       : angle       4.14660 /  3.96 ( 1507)
  Misc. bond           : bond        0.00038 /  0.02 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7119 (tp-100) cc_final: 0.6546 (tm-30)
REVERT: A   43 ARG cc_start: 0.7103 (tpp80) cc_final: 0.6240 (mmm-85)
REVERT: A  537 MET cc_start: 0.7907 (mtp) cc_final: 0.7705 (mtp)
REVERT: A  568 MET cc_start: 0.7931 (mpp) cc_final: 0.7346 (mtp)
REVERT: A  604 MET cc_start: 0.7058 (mmt) cc_final: 0.6406 (mmt)
REVERT: A  720 HIS cc_start: 0.7245 (t-90) cc_final: 0.6896 (t70)
REVERT: A  798 MET cc_start: 0.6288 (tmm) cc_final: 0.5950 (tmm)
REVERT: A  841 GLU cc_start: 0.7185 (pm20) cc_final: 0.6948 (pm20)
REVERT: A  860 LYS cc_start: 0.8312 (tmmt) cc_final: 0.7755 (tmmt)
REVERT: A  861 ASP cc_start: 0.7368 (m-30) cc_final: 0.7001 (m-30)
REVERT: A  949 LYS cc_start: 0.6875 (tptp) cc_final: 0.6387 (tptp)
REVERT: A  971 TYR cc_start: 0.7601 (t80) cc_final: 0.7133 (t80)
REVERT: A 1021 ASP cc_start: 0.7072 (m-30) cc_final: 0.6769 (m-30)
REVERT: A 1099 GLU cc_start: 0.7100 (tp30) cc_final: 0.6720 (tp30)
REVERT: A 1215 MET cc_start: 0.8023 (tpp) cc_final: 0.7728 (tpp)
REVERT: A 1232 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7154 (p)
REVERT: A 1242 ARG cc_start: 0.6917 (ptp-110) cc_final: 0.6646 (ptp-110)
  outliers start: 21
  outliers final: 16
  residues processed: 171
  average time/residue: 0.1411
  time to fit residues: 32.6588
Evaluate side-chains
  177 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  739 LYS
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  937 GLN
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1232 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0670
   chunk 26 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 115 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0270
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 647 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.188801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.147744 restraints weight = 17290.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.149067 restraints weight = 8669.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.149788 restraints weight = 6388.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150090 restraints weight = 5402.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.150480 restraints weight = 5194.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11569  Z= 0.126
  Angle     :  0.533   7.783  15886  Z= 0.282
  Chirality :  0.041   0.291   1772
  Planarity :  0.004   0.046   1836
  Dihedral  : 18.825 170.169   2073
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.88 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.25), residues: 1226
  helix:  1.89 (0.22), residues: 619
  sheet: -0.97 (0.41), residues: 135
  loop : -0.35 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 862 
 TYR   0.025   0.001   TYR A 879 
 PHE   0.022   0.001   PHE A1103 
 TRP   0.008   0.001   TRP A 676 
 HIS   0.012   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.13 (11566)
  covalent geometry    : angle       0.53264 /  0.28 (15886)
  hydrogen bonds       : bond        0.03357 /  3.27 (  539)
  hydrogen bonds       : angle       3.97051 /  3.79 ( 1507)
  Misc. bond           : bond        0.00037 /  0.02 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7030 (tp-100) cc_final: 0.6519 (tm-30)
REVERT: A  568 MET cc_start: 0.7852 (mpp) cc_final: 0.7230 (mtp)
REVERT: A  720 HIS cc_start: 0.7124 (t-90) cc_final: 0.6825 (t70)
REVERT: A  798 MET cc_start: 0.6281 (tmm) cc_final: 0.5941 (tmm)
REVERT: A  841 GLU cc_start: 0.7234 (pm20) cc_final: 0.6973 (pm20)
REVERT: A  860 LYS cc_start: 0.8333 (tmmt) cc_final: 0.7829 (tmmt)
REVERT: A  861 ASP cc_start: 0.7406 (m-30) cc_final: 0.7096 (m-30)
REVERT: A  862 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7667 (ptm160)
REVERT: A  949 LYS cc_start: 0.6875 (tptp) cc_final: 0.6400 (tptp)
REVERT: A  971 TYR cc_start: 0.7591 (t80) cc_final: 0.7105 (t80)
REVERT: A 1021 ASP cc_start: 0.6934 (m-30) cc_final: 0.6700 (m-30)
REVERT: A 1099 GLU cc_start: 0.7106 (tp30) cc_final: 0.6687 (tp30)
REVERT: A 1215 MET cc_start: 0.8013 (tpp) cc_final: 0.7733 (tpp)
REVERT: A 1242 ARG cc_start: 0.6897 (ptp-110) cc_final: 0.6632 (ptp-110)
  outliers start: 21
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1325
  time to fit residues: 32.1057
Evaluate side-chains
  183 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  937 GLN
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1174 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:   50.0000
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 647 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.187118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.144163 restraints weight = 16856.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147569 restraints weight = 8117.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.149741 restraints weight = 5180.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150794 restraints weight = 4007.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.151603 restraints weight = 3524.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11569  Z= 0.199
  Angle     :  0.570   7.201  15886  Z= 0.302
  Chirality :  0.043   0.299   1772
  Planarity :  0.004   0.050   1836
  Dihedral  : 18.866 168.577   2073
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.16 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.25), residues: 1226
  helix:  1.90 (0.22), residues: 622
  sheet: -0.90 (0.41), residues: 133
  loop : -0.39 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 951 
 TYR   0.025   0.002   TYR A 879 
 PHE   0.025   0.002   PHE A1103 
 TRP   0.010   0.002   TRP A 544 
 HIS   0.009   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.20 (11566)
  covalent geometry    : angle       0.56967 /  0.30 (15886)
  hydrogen bonds       : bond        0.03654 /  3.66 (  539)
  hydrogen bonds       : angle       4.00831 /  3.80 ( 1507)
  Misc. bond           : bond        0.00058 /  0.03 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7222 (tp-100) cc_final: 0.6554 (tm-30)
REVERT: A   43 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6326 (mmm-85)
REVERT: A   44 ASN cc_start: 0.7591 (t0) cc_final: 0.7202 (t0)
REVERT: A  516 LYS cc_start: 0.6527 (tttt) cc_final: 0.6012 (tttp)
REVERT: A  568 MET cc_start: 0.7931 (mpp) cc_final: 0.7467 (mtp)
REVERT: A  720 HIS cc_start: 0.7280 (t-90) cc_final: 0.6922 (t70)
REVERT: A  798 MET cc_start: 0.6310 (tmm) cc_final: 0.6032 (tmm)
REVERT: A  841 GLU cc_start: 0.7117 (pm20) cc_final: 0.6911 (pm20)
REVERT: A  860 LYS cc_start: 0.8346 (tmmt) cc_final: 0.7794 (tmmt)
REVERT: A  861 ASP cc_start: 0.7511 (m-30) cc_final: 0.7154 (m-30)
REVERT: A  908 ASP cc_start: 0.7384 (t0) cc_final: 0.7098 (t0)
REVERT: A  949 LYS cc_start: 0.6904 (tptp) cc_final: 0.6378 (tptp)
REVERT: A  971 TYR cc_start: 0.7571 (t80) cc_final: 0.7023 (t80)
REVERT: A 1021 ASP cc_start: 0.7092 (m-30) cc_final: 0.6780 (m-30)
REVERT: A 1099 GLU cc_start: 0.7171 (tp30) cc_final: 0.6635 (tp30)
REVERT: A 1188 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: A 1195 ASP cc_start: 0.7656 (p0) cc_final: 0.7396 (p0)
REVERT: A 1215 MET cc_start: 0.8032 (tpp) cc_final: 0.7725 (tpp)
REVERT: A 1242 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6740 (ptp-110)
  outliers start: 24
  outliers final: 21
  residues processed: 172
  average time/residue: 0.1335
  time to fit residues: 30.9878
Evaluate side-chains
  182 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  925 LYS
Chi-restraints excluded: chain A residue  937 GLN
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1001 SER
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1155 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 118 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 125 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 647 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.187433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146721 restraints weight = 16953.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.150024 restraints weight = 8207.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.151805 restraints weight = 5201.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.153199 restraints weight = 4061.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.153669 restraints weight = 3503.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11569  Z= 0.172
  Angle     :  0.556   8.267  15886  Z= 0.296
  Chirality :  0.042   0.295   1772
  Planarity :  0.004   0.051   1836
  Dihedral  : 18.830 168.998   2073
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.99 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.25), residues: 1226
  helix:  1.90 (0.21), residues: 622
  sheet: -1.00 (0.41), residues: 135
  loop : -0.38 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 955 
 TYR   0.027   0.002   TYR A 879 
 PHE   0.023   0.001   PHE A1103 
 TRP   0.008   0.001   TRP A1085 
 HIS   0.010   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 (11566)
  covalent geometry    : angle       0.55635 /  0.30 (15886)
  hydrogen bonds       : bond        0.03516 /  3.51 (  539)
  hydrogen bonds       : angle       3.96887 /  3.77 ( 1507)
  Misc. bond           : bond        0.00044 /  0.02 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 PHE cc_start: 0.7156 (t80) cc_final: 0.6916 (t80)
REVERT: A  568 MET cc_start: 0.7930 (mpp) cc_final: 0.7440 (mtp)
REVERT: A  720 HIS cc_start: 0.7282 (t-90) cc_final: 0.7033 (t70)
REVERT: A  798 MET cc_start: 0.6313 (tmm) cc_final: 0.6014 (tmm)
REVERT: A  841 GLU cc_start: 0.7096 (pm20) cc_final: 0.6885 (mp0)
REVERT: A  860 LYS cc_start: 0.8344 (tmmt) cc_final: 0.7710 (tmmt)
REVERT: A  861 ASP cc_start: 0.7562 (m-30) cc_final: 0.7212 (m-30)
REVERT: A  862 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7797 (ttp80)
REVERT: A  908 ASP cc_start: 0.7391 (t0) cc_final: 0.7098 (t0)
REVERT: A  949 LYS cc_start: 0.6961 (tptp) cc_final: 0.6353 (tptp)
REVERT: A  971 TYR cc_start: 0.7548 (t80) cc_final: 0.7003 (t80)
REVERT: A 1021 ASP cc_start: 0.7078 (m-30) cc_final: 0.6761 (m-30)
REVERT: A 1099 GLU cc_start: 0.7156 (tp30) cc_final: 0.6622 (tp30)
REVERT: A 1188 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7064 (tm-30)
REVERT: A 1215 MET cc_start: 0.8017 (tpp) cc_final: 0.7711 (tpp)
REVERT: A 1242 ARG cc_start: 0.6969 (ptp-110) cc_final: 0.6721 (ptp-110)
  outliers start: 22
  outliers final: 17
  residues processed: 169
  average time/residue: 0.1264
  time to fit residues: 29.1015
Evaluate side-chains
  172 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1281 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 ASN
A 666 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 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 = 0.4187 r_free = 0.4187 target = 0.186898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.146236 restraints weight = 16857.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.149447 restraints weight = 8142.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151443 restraints weight = 5200.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.152472 restraints weight = 4030.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.153206 restraints weight = 3527.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11569  Z= 0.181
  Angle     :  0.572   8.833  15886  Z= 0.304
  Chirality :  0.043   0.297   1772
  Planarity :  0.005   0.137   1836
  Dihedral  : 18.841 169.291   2073
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.54 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.25), residues: 1226
  helix:  1.88 (0.21), residues: 623
  sheet: -1.00 (0.41), residues: 135
  loop : -0.42 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A  43 
 TYR   0.030   0.002   TYR A 879 
 PHE   0.107   0.002   PHE A 165 
 TRP   0.008   0.001   TRP A1085 
 HIS   0.010   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.18 (11566)
  covalent geometry    : angle       0.57184 /  0.30 (15886)
  hydrogen bonds       : bond        0.03514 /  3.50 (  539)
  hydrogen bonds       : angle       3.97323 /  3.79 ( 1507)
  Misc. bond           : bond        0.00353 /  0.18 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.7007 (t80)
REVERT: A  516 LYS cc_start: 0.6542 (tttt) cc_final: 0.6121 (tttp)
REVERT: A  568 MET cc_start: 0.7923 (mpp) cc_final: 0.7464 (mtp)
REVERT: A  720 HIS cc_start: 0.7288 (t-90) cc_final: 0.7035 (t70)
REVERT: A  798 MET cc_start: 0.6335 (tmm) cc_final: 0.6046 (tmm)
REVERT: A  841 GLU cc_start: 0.7112 (pm20) cc_final: 0.6902 (pm20)
REVERT: A  860 LYS cc_start: 0.8360 (tmmt) cc_final: 0.7702 (tmmt)
REVERT: A  861 ASP cc_start: 0.7577 (m-30) cc_final: 0.7233 (m-30)
REVERT: A  862 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7785 (ttp80)
REVERT: A  908 ASP cc_start: 0.7395 (t0) cc_final: 0.7148 (t0)
REVERT: A  921 ASP cc_start: 0.7182 (p0) cc_final: 0.6937 (p0)
REVERT: A  949 LYS cc_start: 0.7018 (tptp) cc_final: 0.6437 (tptp)
REVERT: A  971 TYR cc_start: 0.7555 (t80) cc_final: 0.6996 (t80)
REVERT: A 1021 ASP cc_start: 0.7067 (m-30) cc_final: 0.6759 (m-30)
REVERT: A 1099 GLU cc_start: 0.7166 (tp30) cc_final: 0.6583 (tp30)
REVERT: A 1188 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7072 (tm-30)
REVERT: A 1215 MET cc_start: 0.8025 (tpp) cc_final: 0.7747 (tpp)
REVERT: A 1242 ARG cc_start: 0.6956 (ptp-110) cc_final: 0.6739 (ptp-110)
  outliers start: 20
  outliers final: 17
  residues processed: 163
  average time/residue: 0.1342
  time to fit residues: 29.3818
Evaluate side-chains
  171 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue 1001 SER
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1281 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 120 optimal weight:    0.5980
   chunk 116 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 121 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0370
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.4458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 ASN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.188277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.147455 restraints weight = 17069.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150736 restraints weight = 8269.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152718 restraints weight = 5279.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153756 restraints weight = 4110.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.154535 restraints weight = 3598.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11569  Z= 0.126
  Angle     :  0.542   8.666  15886  Z= 0.290
  Chirality :  0.041   0.291   1772
  Planarity :  0.005   0.086   1836
  Dihedral  : 18.753 170.641   2073
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.01 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.25), residues: 1226
  helix:  1.90 (0.21), residues: 624
  sheet: -0.96 (0.41), residues: 135
  loop : -0.35 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 951 
 TYR   0.029   0.001   TYR A 879 
 PHE   0.083   0.002   PHE A 165 
 TRP   0.007   0.001   TRP A 676 
 HIS   0.012   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 (11566)
  covalent geometry    : angle       0.54236 /  0.29 (15886)
  hydrogen bonds       : bond        0.03247 /  3.18 (  539)
  hydrogen bonds       : angle       3.89423 /  3.73 ( 1507)
  Misc. bond           : bond        0.00414 /  0.21 (    3)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7336 (tp30) cc_final: 0.6998 (tp30)
REVERT: A  513 PHE cc_start: 0.7271 (t80) cc_final: 0.6993 (t80)
REVERT: A  568 MET cc_start: 0.7875 (mpp) cc_final: 0.7382 (mtp)
REVERT: A  720 HIS cc_start: 0.7184 (t-90) cc_final: 0.6813 (t70)
REVERT: A  798 MET cc_start: 0.6396 (tmm) cc_final: 0.6085 (tmm)
REVERT: A  841 GLU cc_start: 0.7039 (pm20) cc_final: 0.6835 (mp0)
REVERT: A  860 LYS cc_start: 0.8343 (tmmt) cc_final: 0.7716 (tmmt)
REVERT: A  861 ASP cc_start: 0.7530 (m-30) cc_final: 0.7202 (m-30)
REVERT: A  862 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7650 (ptm160)
REVERT: A  921 ASP cc_start: 0.7152 (p0) cc_final: 0.6906 (p0)
REVERT: A  949 LYS cc_start: 0.6867 (tptp) cc_final: 0.6310 (tptp)
REVERT: A  971 TYR cc_start: 0.7520 (t80) cc_final: 0.6988 (t80)
REVERT: A 1021 ASP cc_start: 0.7024 (m-30) cc_final: 0.6737 (m-30)
REVERT: A 1099 GLU cc_start: 0.7116 (tp30) cc_final: 0.6555 (tp30)
REVERT: A 1129 LEU cc_start: 0.7939 (mm) cc_final: 0.7698 (mt)
REVERT: A 1188 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7038 (tm-30)
REVERT: A 1215 MET cc_start: 0.8023 (tpp) cc_final: 0.7767 (tpp)
  outliers start: 17
  outliers final: 17
  residues processed: 164
  average time/residue: 0.1343
  time to fit residues: 29.7805
Evaluate side-chains
  170 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1001 SER
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1281 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:   20.0000
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 ASN
A1105 HIS
** A1227 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 = 0.4206 r_free = 0.4206 target = 0.189968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150112 restraints weight = 16893.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150214 restraints weight = 9625.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.151204 restraints weight = 6679.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.151371 restraints weight = 6079.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.151597 restraints weight = 5445.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11569  Z= 0.209
  Angle     :  0.596  12.029  15886  Z= 0.313
  Chirality :  0.043   0.301   1772
  Planarity :  0.004   0.053   1836
  Dihedral  : 18.808 168.958   2073
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.54 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.95 (0.25), residues: 1226
  helix:  1.78 (0.21), residues: 630
  sheet: -0.91 (0.42), residues: 135
  loop : -0.43 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 951 
 TYR   0.024   0.002   TYR A 595 
 PHE   0.067   0.002   PHE A 165 
 TRP   0.010   0.001   TRP A 544 
 HIS   0.013   0.001   HIS A1091 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.21 (11566)
  covalent geometry    : angle       0.59563 /  0.31 (15886)
  hydrogen bonds       : bond        0.03539 /  3.57 (  539)
  hydrogen bonds       : angle       3.97810 /  3.81 ( 1507)
  Misc. bond           : bond        0.00327 /  0.16 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1995.70 seconds
wall clock time: 35 minutes 16.06 seconds (2116.06 seconds total)