Starting phenix.real_space_refine
on Wed Feb  4 17:36:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s4u_24833/02_2026/7s4u_24833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s4u_24833/02_2026/7s4u_24833.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s4u_24833/02_2026/7s4u_24833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s4u_24833/02_2026/7s4u_24833.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s4u_24833/02_2026/7s4u_24833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s4u_24833/02_2026/7s4u_24833.cif"
  }
  resolution = 3.56
  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=   0.107
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     142      5.49       5
     S      16      5.16       5
     C    7078      2.51       5
     N    2093      2.21       5
     O    2598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11927
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1092, 8928
          Classifications: {'peptide': 1092}
          Link IDs: {'PTRANS': 29, 'TRANS': 1062}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 2080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 2080
          Classifications: {'RNA': 97}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 48, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 17, 'rna3p': 79}
    Chain: "C"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 648
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "D"
      Number of atoms: 271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 271
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
  Time building chain proxies: 2.87, per 1000 atoms: 0.24
  Number of scatterers: 11927
  At special positions: 0
  Unit cell: (89.1, 130.9, 145.2, 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      16     16.00
     P     142     15.00
     O    2598      8.00
     N    2093      7.00
     C    7078      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 437.1 milliseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 5 sheets defined
      58.2% alpha, 8.4% beta
      38 base pairs and 76 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 91
      removed outlier: 3.794A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ASN A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 101
      removed outlier: 3.572A  pdb=" N   LEU A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 135 through 144
      removed outlier: 3.612A  pdb=" N   LYS A 141 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.653A  pdb=" N   HIS A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   MET A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.547A  pdb=" N   SER A 179 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.597A  pdb=" N   ALA A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 237 through 246
      removed outlier: 4.775A  pdb=" N   ALA A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 262
      removed outlier: 3.697A  pdb=" N   ASP A 261 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 3.649A  pdb=" N   GLN A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 306
      removed outlier: 4.112A  pdb=" N   ASN A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASP A 304 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.537A  pdb=" N   ILE A 322 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   HIS A 328 " --> pdb=" O   ARG A 324 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 334 " --> pdb=" O   GLN A 330 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 337 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 351
      removed outlier: 3.722A  pdb=" N   TYR A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LYS A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.698A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.278A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
      removed outlier: 4.009A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASP A 435 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 430 through 435'
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 474 through 478
      removed outlier: 3.567A  pdb=" N   ASN A 477 " --> pdb=" O   THR A 474 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE A 478 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 474 through 478'
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 3.920A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 562 through 573
      removed outlier: 3.514A  pdb=" N   GLU A 566 " --> pdb=" O   LYS A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 608
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 4.188A  pdb=" N   ASP A 618 " --> pdb=" O   ASP A 614 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 668
      removed outlier: 3.720A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 687 through 691
      removed outlier: 3.524A  pdb=" N   ARG A 691 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 700
      removed outlier: 3.917A  pdb=" N   HIS A 698 " --> pdb=" O   MET A 694 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 710
      removed outlier: 5.729A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ASP A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ILE A 708 " --> pdb=" O   PHE A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 724
    Processing helix  chain 'A' and resid 725 through 727
      No H-bonds generated for 'chain 'A' and resid 725 through 727'
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.850A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.572A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 932 " --> pdb=" O   THR A 928 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG A 938 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.266A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1000
    Processing helix  chain 'A' and resid 1076 through 1089
      removed outlier: 4.189A  pdb=" N   PHE A1080 " --> pdb=" O   LYS A1076 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ALA A1081 " --> pdb=" O   GLY A1077 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   THR A1082 " --> pdb=" O   ARG A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1186
      removed outlier: 3.532A  pdb=" N   GLY A1186 " --> pdb=" O   LEU A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
      removed outlier: 3.585A  pdb=" N   VAL A1233 " --> pdb=" O   PRO A1229 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A1238 " --> pdb=" O   ASN A1234 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A1239 " --> pdb=" O   PHE A1235 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   HIS A1241 " --> pdb=" O   TYR A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1260
      removed outlier: 4.191A  pdb=" N   GLN A1254 " --> pdb=" O   GLU A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.883A  pdb=" N   ASN A1308 " --> pdb=" O   GLU A1304 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1338 through 1343
      removed outlier: 3.605A  pdb=" N   LEU A1343 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.397A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TRP A  18 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 3.655A  pdb=" N   LYS A  30 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 10.524A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1106 through 1111
      removed outlier: 6.938A  pdb=" N   LYS A1107 " --> pdb=" O   PRO A1137 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   SER A1109 " --> pdb=" O   ASP A1135 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   ASP A1135 " --> pdb=" O   SER A1109 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A1133 " --> pdb=" O   LEU A1111 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.667A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326

    385 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      97 hydrogen bonds
      194 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      76 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 1.47 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: 2410
        1.33 -     1.45: 3417
        1.45 -     1.57: 6303
        1.57 -     1.69: 281
        1.69 -     1.81: 31
  Bond restraints: 12442
  Sorted by residual:
  bond pdb=" N   ASP A 686 "
       pdb=" CA  ASP A 686 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.030 1.31e-02 5.83e+03 5.27e+00
  bond pdb=" CA  LYS A 348 "
       pdb=" C   LYS A 348 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.027 1.41e-02 5.03e+03 3.77e+00
  bond pdb=" CA  GLY A1165 "
       pdb=" C   GLY A1165 "
    ideal  model  delta    sigma   weight residual
    1.518  1.529 -0.011 7.30e-03 1.88e+04 2.14e+00
  bond pdb=" C   SER A 685 "
       pdb=" N   ASP A 686 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.37e-02 5.33e+03 2.12e+00
  bond pdb=" CA  ILE A 448 "
       pdb=" C   ILE A 448 "
    ideal  model  delta    sigma   weight residual
    1.527  1.515  0.011 8.00e-03 1.56e+04 2.01e+00
  ... (remaining 12437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 16941
        1.97 -     3.94: 411
        3.94 -     5.91: 50
        5.91 -     7.88: 10
        7.88 -     9.85: 1
  Bond angle restraints: 17413
  Sorted by residual:
  angle pdb=" C3'   C B  90 "
        pdb=" O3'   C B  90 "
        pdb=" P     G B  91 "
      ideal   model   delta    sigma   weight residual
     120.20  126.48   -6.28 1.50e+00 4.44e-01 1.75e+01
  angle pdb=" C3'   C B   2 "
        pdb=" O3'   C B   2 "
        pdb=" P     G B   3 "
      ideal   model   delta    sigma   weight residual
     120.20  125.75   -5.55 1.50e+00 4.44e-01 1.37e+01
  angle pdb=" O3'   C B  90 "
        pdb=" C3'   C B  90 "
        pdb=" C2'   C B  90 "
      ideal   model   delta    sigma   weight residual
     113.70  119.04   -5.34 1.50e+00 4.44e-01 1.27e+01
  angle pdb=" C2'   G B   3 "
        pdb=" C1'   G B   3 "
        pdb=" N9    G B   3 "
      ideal   model   delta    sigma   weight residual
     112.00  117.12   -5.12 1.50e+00 4.44e-01 1.17e+01
  angle pdb=" N   ILE A 615 "
        pdb=" CA  ILE A 615 "
        pdb=" C   ILE A 615 "
      ideal   model   delta    sigma   weight residual
     111.45  108.31    3.14 9.30e-01 1.16e+00 1.14e+01
  ... (remaining 17408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.30: 7084
       35.30 -    70.60: 400
       70.60 -   105.90: 41
      105.90 -   141.20: 4
      141.20 -   176.49: 4
  Dihedral angle restraints: 7533
    sinusoidal: 4321
      harmonic: 3212
  Sorted by residual:
  dihedral pdb=" C4'   A B   1 "
           pdb=" C3'   A B   1 "
           pdb=" C2'   A B   1 "
           pdb=" C1'   A B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   34.21  -69.21     1      8.00e+00 1.56e-02 9.68e+01
  dihedral pdb=" C5'   A B   1 "
           pdb=" C4'   A B   1 "
           pdb=" C3'   A B   1 "
           pdb=" O3'   A B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   82.33   64.67     1      8.00e+00 1.56e-02 8.58e+01
  dihedral pdb=" O4'   C B  69 "
           pdb=" C1'   C B  69 "
           pdb=" N1    C B  69 "
           pdb=" C2    C B  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.22  149.78     1      1.50e+01 4.44e-03 7.95e+01
  ... (remaining 7530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1794
       0.065 -    0.129: 212
       0.129 -    0.194: 13
       0.194 -    0.259: 2
       0.259 -    0.324: 1
  Chirality restraints: 2022
  Sorted by residual:
  chirality pdb=" C3'   A B   1 "
            pdb=" C4'   A B   1 "
            pdb=" O3'   A B   1 "
            pdb=" C2'   A B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.42   -0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" C1'   G B   3 "
            pdb=" O4'   G B   3 "
            pdb=" C2'   G B   3 "
            pdb=" N9    G B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.20    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" C2'   A B   1 "
            pdb=" C3'   A B   1 "
            pdb=" O2'   A B   1 "
            pdb=" C1'   A B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.73    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 2019 not shown)

  Planarity restraints: 1694
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   3 "   -0.036 2.00e-02 2.50e+03   1.61e-02 7.78e+00
        pdb=" N9    G B   3 "    0.040 2.00e-02 2.50e+03
        pdb=" C8    G B   3 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G B   3 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G B   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B   3 "   -0.008 2.00e-02 2.50e+03
        pdb=" O6    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G B   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G B   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B   3 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    G B   3 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   7 "   -0.028 2.00e-02 2.50e+03   1.30e-02 4.66e+00
        pdb=" N9    A B   7 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    A B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    A B   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    A B   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6    A B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A B   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A B   7 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A B   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A B   7 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C  35 "    0.028 2.00e-02 2.50e+03   1.18e-02 4.16e+00
        pdb=" N9   DG C  35 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8   DG C  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG C  35 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG C  35 "    0.005 2.00e-02 2.50e+03
        pdb=" O6   DG C  35 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG C  35 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG C  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG C  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DG C  35 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1691 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 251
        2.65 -     3.21: 10971
        3.21 -     3.78: 18440
        3.78 -     4.34: 25014
        4.34 -     4.90: 38258
  Nonbonded interactions: 92934
  Sorted by model distance:
  nonbonded pdb=" O2'   C B  90 "
            pdb=" OP1   G B  91 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" OG  SER A 541 "
            pdb=" OD2 ASP A 686 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OD1 ASN A  14 "
            pdb=" OG  SER A  55 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR A 373 "
            pdb=" O   LEU A 398 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O2'   A B  37 "
            pdb=" OP1   G B  38 "
     model   vdw
     2.200 3.040
  ... (remaining 92929 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.92
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:             4.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.330
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
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   0.033  12442  Z= 0.190
  Angle     :  0.737   9.851  17413  Z= 0.413
  Chirality :  0.042   0.324   2022
  Planarity :  0.004   0.042   1694
  Dihedral  : 19.562 176.495   5447
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.09 (0.25), residues: 1076
  helix: -0.75 (0.22), residues: 517
  sheet: -0.15 (0.52), residues: 106
  loop : -0.61 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 664 
 TYR   0.026   0.002   TYR A 362 
 PHE   0.025   0.002   PHE A 478 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.007   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12442)
  covalent geometry    : angle       0.73673 (17413)
  hydrogen bonds       : bond        0.16339 (  482)
  hydrogen bonds       : angle       6.30250 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.398 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1347
  time to fit residues: 15.1054
Evaluate side-chains
  47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
A  83 GLN
A 402 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.132203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.101622 restraints weight = 23096.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.104147 restraints weight = 51016.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.104128 restraints weight = 21191.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.105421 restraints weight = 17059.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.105428 restraints weight = 13718.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12442  Z= 0.203
  Angle     :  0.702   8.416  17413  Z= 0.372
  Chirality :  0.043   0.231   2022
  Planarity :  0.004   0.038   1694
  Dihedral  : 21.444 170.723   3131
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  4.49 %
    Favored  : 94.90 %
  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: 1076
  helix: -0.55 (0.22), residues: 528
  sheet: -0.49 (0.52), residues: 107
  loop : -0.74 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1298 
 TYR   0.028   0.002   TYR A 362 
 PHE   0.028   0.002   PHE A 704 
 TRP   0.019   0.002   TRP A  18 
 HIS   0.007   0.002   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (12442)
  covalent geometry    : angle       0.70216 (17413)
  hydrogen bonds       : bond        0.06440 (  482)
  hydrogen bonds       : angle       4.85935 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 57
  average time/residue: 0.1429
  time to fit residues: 11.2922
Evaluate side-chains
  50 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue 1085 LYS
Chi-restraints excluded: chain A residue 1092 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 98 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.133757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.103197 restraints weight = 23164.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.105651 restraints weight = 50927.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.105766 restraints weight = 20543.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107041 restraints weight = 16390.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107082 restraints weight = 13101.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12442  Z= 0.143
  Angle     :  0.601   9.415  17413  Z= 0.317
  Chirality :  0.039   0.223   2022
  Planarity :  0.004   0.037   1694
  Dihedral  : 21.077 173.665   3131
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  6.02 %
    Favored  : 92.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.25), residues: 1076
  helix: -0.25 (0.22), residues: 537
  sheet: -0.47 (0.52), residues: 108
  loop : -0.69 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1298 
 TYR   0.021   0.002   TYR A 362 
 PHE   0.021   0.001   PHE A 256 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12442)
  covalent geometry    : angle       0.60060 (17413)
  hydrogen bonds       : bond        0.05202 (  482)
  hydrogen bonds       : angle       4.45444 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.7990 (mmt) cc_final: 0.7643 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1597
  time to fit residues: 12.9494
Evaluate side-chains
  52 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 117 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.130830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.098595 restraints weight = 23228.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.100701 restraints weight = 50998.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.101021 restraints weight = 24240.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.102070 restraints weight = 17682.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.102286 restraints weight = 15460.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12442  Z= 0.224
  Angle     :  0.672   9.148  17413  Z= 0.353
  Chirality :  0.041   0.236   2022
  Planarity :  0.004   0.040   1694
  Dihedral  : 21.154 169.365   3131
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  7.45 %
    Favored  : 91.63 %
  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: -0.96 (0.25), residues: 1076
  helix: -0.23 (0.22), residues: 526
  sheet: -0.67 (0.53), residues: 106
  loop : -0.97 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.029   0.002   TYR A 362 
 PHE   0.020   0.002   PHE A1324 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.006   0.002   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (12442)
  covalent geometry    : angle       0.67245 (17413)
  hydrogen bonds       : bond        0.06664 (  482)
  hydrogen bonds       : angle       4.67052 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  925 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7234 (tpp80)
  outliers start: 9
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1488
  time to fit residues: 11.9103
Evaluate side-chains
  57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue  986 ASP
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 83 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 34 optimal weight:    0.3980
   chunk 119 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0270
   chunk 110 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 105 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.133697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.102166 restraints weight = 23134.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.104766 restraints weight = 50814.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.105153 restraints weight = 21814.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.105837 restraints weight = 16815.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.106106 restraints weight = 15101.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12442  Z= 0.129
  Angle     :  0.563   9.513  17413  Z= 0.297
  Chirality :  0.037   0.221   2022
  Planarity :  0.003   0.038   1694
  Dihedral  : 20.892 173.027   3131
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.57 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.26), residues: 1076
  helix:  0.10 (0.23), residues: 526
  sheet: -0.59 (0.52), residues: 107
  loop : -0.76 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1298 
 TYR   0.019   0.001   TYR A 362 
 PHE   0.011   0.001   PHE A 518 
 TRP   0.013   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (12442)
  covalent geometry    : angle       0.56331 (17413)
  hydrogen bonds       : bond        0.04770 (  482)
  hydrogen bonds       : angle       4.24328 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8037 (mmt) cc_final: 0.7688 (mmm)
REVERT: A  925 ARG cc_start: 0.7413 (tpp80) cc_final: 0.7131 (tpp80)
  outliers start: 11
  outliers final: 6
  residues processed: 66
  average time/residue: 0.1366
  time to fit residues: 12.6359
Evaluate side-chains
  57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 87 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.133309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.102866 restraints weight = 23153.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.105387 restraints weight = 52265.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.105637 restraints weight = 21146.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.106863 restraints weight = 16538.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.106965 restraints weight = 13238.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12442  Z= 0.136
  Angle     :  0.575   9.462  17413  Z= 0.302
  Chirality :  0.037   0.224   2022
  Planarity :  0.003   0.040   1694
  Dihedral  : 20.848 172.836   3131
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.39 %
    Favored  : 89.39 %
  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: -0.51 (0.26), residues: 1076
  helix:  0.15 (0.23), residues: 526
  sheet: -0.47 (0.53), residues: 106
  loop : -0.75 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1298 
 TYR   0.021   0.001   TYR A 362 
 PHE   0.021   0.001   PHE A 704 
 TRP   0.012   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (12442)
  covalent geometry    : angle       0.57524 (17413)
  hydrogen bonds       : bond        0.04921 (  482)
  hydrogen bonds       : angle       4.24574 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7384 (tpp) cc_final: 0.6728 (tpp)
REVERT: A  321 MET cc_start: 0.7988 (mmt) cc_final: 0.7662 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1397
  time to fit residues: 12.1974
Evaluate side-chains
  61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 112 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0010
   chunk 34 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.134231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.103552 restraints weight = 23052.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.105804 restraints weight = 50309.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.106268 restraints weight = 21130.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.107081 restraints weight = 16525.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.107328 restraints weight = 13931.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12442  Z= 0.123
  Angle     :  0.547   9.188  17413  Z= 0.288
  Chirality :  0.036   0.219   2022
  Planarity :  0.003   0.039   1694
  Dihedral  : 20.777 173.751   3131
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.69 %
    Favored  : 88.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.43 (0.26), residues: 1076
  helix:  0.22 (0.23), residues: 529
  sheet: -0.41 (0.53), residues: 105
  loop : -0.74 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1298 
 TYR   0.018   0.001   TYR A 362 
 PHE   0.013   0.001   PHE A 518 
 TRP   0.012   0.002   TRP A  18 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (12442)
  covalent geometry    : angle       0.54668 (17413)
  hydrogen bonds       : bond        0.04496 (  482)
  hydrogen bonds       : angle       4.12813 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7381 (tpp) cc_final: 0.6723 (tpp)
  outliers start: 14
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1237
  time to fit residues: 11.7354
Evaluate side-chains
  59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1254 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 86 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 117 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.132678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.099906 restraints weight = 23127.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.101892 restraints weight = 49935.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.102630 restraints weight = 24148.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103263 restraints weight = 17637.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103698 restraints weight = 15900.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12442  Z= 0.158
  Angle     :  0.588   8.819  17413  Z= 0.308
  Chirality :  0.038   0.228   2022
  Planarity :  0.004   0.041   1694
  Dihedral  : 20.819 171.890   3131
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.90 %
    Favored  : 88.98 %
  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: -0.54 (0.26), residues: 1076
  helix:  0.15 (0.23), residues: 528
  sheet: -0.53 (0.52), residues: 106
  loop : -0.80 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1298 
 TYR   0.023   0.002   TYR A 362 
 PHE   0.022   0.001   PHE A 704 
 TRP   0.011   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12442)
  covalent geometry    : angle       0.58761 (17413)
  hydrogen bonds       : bond        0.05347 (  482)
  hydrogen bonds       : angle       4.29869 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8010 (mmt) cc_final: 0.7652 (mmm)
  outliers start: 11
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1404
  time to fit residues: 12.3070
Evaluate side-chains
  60 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1331 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 44 optimal weight:    0.1980
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 65 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN
A 983 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.131682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.099692 restraints weight = 23179.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.101664 restraints weight = 50746.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.102433 restraints weight = 23164.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.102957 restraints weight = 17516.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.103336 restraints weight = 15624.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12442  Z= 0.191
  Angle     :  0.626   8.293  17413  Z= 0.329
  Chirality :  0.040   0.233   2022
  Planarity :  0.004   0.045   1694
  Dihedral  : 20.888 170.011   3131
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.61 %
    Favored  : 88.47 %
  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: -0.70 (0.26), residues: 1076
  helix:  0.03 (0.23), residues: 528
  sheet: -0.59 (0.53), residues: 104
  loop : -0.89 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1298 
 TYR   0.025   0.002   TYR A 362 
 PHE   0.017   0.002   PHE A1324 
 TRP   0.009   0.002   TRP A  18 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (12442)
  covalent geometry    : angle       0.62633 (17413)
  hydrogen bonds       : bond        0.06023 (  482)
  hydrogen bonds       : angle       4.42242 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7456 (tpp) cc_final: 0.6792 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 62
  average time/residue: 0.1452
  time to fit residues: 12.4454
Evaluate side-chains
  60 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1331 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 80 optimal weight:    0.0770
   chunk 22 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0870
   chunk 68 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 107 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.134241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.104122 restraints weight = 23025.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.106558 restraints weight = 50660.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.106647 restraints weight = 20608.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.107860 restraints weight = 16197.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.107941 restraints weight = 12923.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12442  Z= 0.120
  Angle     :  0.549   7.976  17413  Z= 0.289
  Chirality :  0.037   0.234   2022
  Planarity :  0.004   0.052   1694
  Dihedral  : 20.757 173.282   3131
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.12 %
    Favored  : 88.16 %
  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: -0.57 (0.26), residues: 1076
  helix:  0.16 (0.23), residues: 530
  sheet: -0.55 (0.53), residues: 105
  loop : -0.85 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1298 
 TYR   0.017   0.001   TYR A 362 
 PHE   0.032   0.001   PHE A 704 
 TRP   0.012   0.001   TRP A  18 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12442)
  covalent geometry    : angle       0.54946 (17413)
  hydrogen bonds       : bond        0.04453 (  482)
  hydrogen bonds       : angle       4.13993 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 5
  residues processed: 61
  average time/residue: 0.1398
  time to fit residues: 12.0500
Evaluate side-chains
  59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1254 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.131649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.099768 restraints weight = 23175.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.102306 restraints weight = 50195.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.102674 restraints weight = 21486.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.103161 restraints weight = 16730.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103709 restraints weight = 14654.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12442  Z= 0.194
  Angle     :  0.623   7.944  17413  Z= 0.326
  Chirality :  0.040   0.232   2022
  Planarity :  0.004   0.046   1694
  Dihedral  : 20.861 170.500   3131
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.92 %
    Favored  : 88.47 %
  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: -0.71 (0.25), residues: 1076
  helix:  0.05 (0.23), residues: 528
  sheet: -0.66 (0.52), residues: 104
  loop : -0.92 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1298 
 TYR   0.025   0.002   TYR A 362 
 PHE   0.017   0.002   PHE A1324 
 TRP   0.011   0.002   TRP A  18 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (12442)
  covalent geometry    : angle       0.62287 (17413)
  hydrogen bonds       : bond        0.05879 (  482)
  hydrogen bonds       : angle       4.40252 ( 1301)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1559.90 seconds
wall clock time: 27 minutes 53.12 seconds (1673.12 seconds total)