Starting phenix.real_space_refine
on Wed Jul 30 08:24:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s4u_24833/07_2025/7s4u_24833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s4u_24833/07_2025/7s4u_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_24833/07_2025/7s4u_24833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2025/7s4u_24833.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2025/7s4u_24833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s4u_24833/07_2025/7s4u_24833.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.08, per 1000 atoms: 0.68
  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: 3.16
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 4.46
  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: 7.28

  Time building geometry restraints manager: 3.76 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:             3.660
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     36.360
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:3.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.360
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (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
 TRP   0.014   0.002   TRP A  18 
 HIS   0.007   0.001   HIS A 412 
 PHE   0.025   0.002   PHE A 478 
 TYR   0.026   0.002   TYR A 362 
 ARG   0.013   0.001   ARG A 664 

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

*********************** 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  : 1.234 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.3079
  time to fit residues: 34.9010
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  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 49 optimal weight:    0.1980
   chunk 95 optimal weight:    0.0570
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0070
   chunk 110 optimal weight:    2.9990
   overall best weight:    0.3716

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.136874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.105444 restraints weight = 22842.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.108214 restraints weight = 49341.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.108698 restraints weight = 20317.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12442  Z= 0.128
  Angle     :  0.606   8.305  17413  Z= 0.322
  Chirality :  0.039   0.218   2022
  Planarity :  0.004   0.035   1694
  Dihedral  : 21.276 175.124   3131
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  3.88 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.26), residues: 1076
  helix: -0.22 (0.22), residues: 535
  sheet: -0.24 (0.52), residues: 106
  loop : -0.33 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  18 
 HIS   0.005   0.001   HIS A 930 
 PHE   0.028   0.001   PHE A 704 
 TYR   0.022   0.002   TYR A   5 
 ARG   0.005   0.001   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04600 (  482)
  hydrogen bonds       : angle       4.51703 ( 1301)
  covalent geometry    : bond        0.00250 (12442)
  covalent geometry    : angle       0.60632 (17413)

*********************** 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
  65 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 63
  average time/residue: 0.3929
  time to fit residues: 33.8498
Evaluate side-chains
  49 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 LEU
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 100 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0170
   chunk 107 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.8024

-------------------------------------------------------------------------------
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
A 726 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.130529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.098329 restraints weight = 23216.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.100297 restraints weight = 51451.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.100866 restraints weight = 24974.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12442  Z= 0.252
  Angle     :  0.717   8.941  17413  Z= 0.376
  Chirality :  0.043   0.237   2022
  Planarity :  0.004   0.039   1694
  Dihedral  : 21.336 170.324   3131
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  5.10 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.25), residues: 1076
  helix: -0.46 (0.22), residues: 536
  sheet: -0.49 (0.52), residues: 107
  loop : -0.82 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  18 
 HIS   0.008   0.002   HIS A 137 
 PHE   0.023   0.002   PHE A1324 
 TYR   0.031   0.002   TYR A 362 
 ARG   0.007   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07226 (  482)
  hydrogen bonds       : angle       4.86488 ( 1301)
  covalent geometry    : bond        0.00569 (12442)
  covalent geometry    : angle       0.71698 (17413)

*********************** 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
  59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 56
  average time/residue: 0.2944
  time to fit residues: 23.7469
Evaluate side-chains
  51 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 118 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   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 = 0.132467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.101873 restraints weight = 22954.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.104758 restraints weight = 48758.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.104544 restraints weight = 19672.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12442  Z= 0.159
  Angle     :  0.608   9.260  17413  Z= 0.320
  Chirality :  0.039   0.226   2022
  Planarity :  0.003   0.037   1694
  Dihedral  : 21.043 171.698   3131
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.14 %
    Favored  : 92.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 1076
  helix: -0.21 (0.22), residues: 532
  sheet: -0.62 (0.52), residues: 108
  loop : -0.75 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  18 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.014   0.001   PHE A1324 
 TYR   0.022   0.002   TYR A 362 
 ARG   0.004   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05456 (  482)
  hydrogen bonds       : angle       4.49548 ( 1301)
  covalent geometry    : bond        0.00346 (12442)
  covalent geometry    : angle       0.60822 (17413)

*********************** 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
  62 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 2.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  661 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7908 (mmp80)
  outliers start: 7
  outliers final: 4
  residues processed: 61
  average time/residue: 0.3341
  time to fit residues: 30.3929
Evaluate side-chains
  52 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 66 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0030
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.133461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.101512 restraints weight = 22797.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.103391 restraints weight = 51469.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.104309 restraints weight = 23508.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12442  Z= 0.129
  Angle     :  0.564   9.509  17413  Z= 0.297
  Chirality :  0.037   0.222   2022
  Planarity :  0.003   0.036   1694
  Dihedral  : 20.881 173.288   3131
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.88 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.26), residues: 1076
  helix:  0.02 (0.23), residues: 526
  sheet: -0.56 (0.52), residues: 107
  loop : -0.69 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  18 
 HIS   0.004   0.001   HIS A 412 
 PHE   0.012   0.001   PHE A 518 
 TYR   0.019   0.001   TYR A 362 
 ARG   0.010   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04772 (  482)
  hydrogen bonds       : angle       4.29020 ( 1301)
  covalent geometry    : bond        0.00271 (12442)
  covalent geometry    : angle       0.56435 (17413)

*********************** 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
  67 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  925 ARG cc_start: 0.7498 (tpp80) cc_final: 0.7176 (tpp80)
  outliers start: 10
  outliers final: 3
  residues processed: 64
  average time/residue: 0.3829
  time to fit residues: 33.7011
Evaluate side-chains
  54 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0270
   chunk 43 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 20 optimal weight:   10.0000
   chunk 105 optimal weight:    0.0980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.134739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.102680 restraints weight = 23247.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.105087 restraints weight = 49849.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.105690 restraints weight = 22223.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12442  Z= 0.116
  Angle     :  0.546   9.433  17413  Z= 0.286
  Chirality :  0.036   0.216   2022
  Planarity :  0.003   0.035   1694
  Dihedral  : 20.766 174.637   3131
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  9.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.25), residues: 1076
  helix:  0.10 (0.23), residues: 529
  sheet: -0.46 (0.51), residues: 107
  loop : -0.68 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  18 
 HIS   0.004   0.001   HIS A 412 
 PHE   0.013   0.001   PHE A 518 
 TYR   0.017   0.001   TYR A 362 
 ARG   0.010   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  482)
  hydrogen bonds       : angle       4.16275 ( 1301)
  covalent geometry    : bond        0.00240 (12442)
  covalent geometry    : angle       0.54631 (17413)

*********************** 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
  67 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  925 ARG cc_start: 0.7434 (tpp80) cc_final: 0.7211 (tpp80)
  outliers start: 9
  outliers final: 3
  residues processed: 66
  average time/residue: 0.3211
  time to fit residues: 29.4778
Evaluate side-chains
  57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    9.9990
   chunk 43 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.132317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100494 restraints weight = 23099.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.103208 restraints weight = 51441.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103582 restraints weight = 21511.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2643

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= 0.173
  Angle     :  0.609   9.166  17413  Z= 0.320
  Chirality :  0.039   0.231   2022
  Planarity :  0.004   0.037   1694
  Dihedral  : 20.848 171.881   3131
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.90 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.26), residues: 1076
  helix:  0.08 (0.23), residues: 527
  sheet: -0.43 (0.52), residues: 106
  loop : -0.79 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A 412 
 PHE   0.026   0.002   PHE A 196 
 TYR   0.025   0.002   TYR A 362 
 ARG   0.010   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05637 (  482)
  hydrogen bonds       : angle       4.38913 ( 1301)
  covalent geometry    : bond        0.00382 (12442)
  covalent geometry    : angle       0.60894 (17413)

*********************** 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
  65 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  925 ARG cc_start: 0.7483 (tpp80) cc_final: 0.7269 (tpp80)
  outliers start: 10
  outliers final: 7
  residues processed: 64
  average time/residue: 0.3338
  time to fit residues: 29.4321
Evaluate side-chains
  60 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
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  959 LYS
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 1331 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 116 optimal weight:    7.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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 = 0.4038 r_free = 0.4038 target = 0.132516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.100644 restraints weight = 23287.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.103191 restraints weight = 51686.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.103690 restraints weight = 21964.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12442  Z= 0.165
  Angle     :  0.603   8.809  17413  Z= 0.317
  Chirality :  0.038   0.228   2022
  Planarity :  0.004   0.040   1694
  Dihedral  : 20.840 171.231   3131
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.82 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1076
  helix:  0.12 (0.23), residues: 526
  sheet: -0.57 (0.51), residues: 106
  loop : -0.87 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  18 
 HIS   0.005   0.001   HIS A 412 
 PHE   0.026   0.001   PHE A 196 
 TYR   0.023   0.002   TYR A 362 
 ARG   0.010   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05453 (  482)
  hydrogen bonds       : angle       4.35700 ( 1301)
  covalent geometry    : bond        0.00364 (12442)
  covalent geometry    : angle       0.60332 (17413)

*********************** 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: 9
    poor density    : 56
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  925 ARG cc_start: 0.7471 (tpp80) cc_final: 0.7265 (tpp80)
  outliers start: 9
  outliers final: 7
  residues processed: 62
  average time/residue: 0.3363
  time to fit residues: 28.6597
Evaluate side-chains
  62 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
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 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 19 optimal weight:    9.9990
   chunk 115 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 117 optimal weight:    8.9990
   chunk 101 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.129488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.099118 restraints weight = 23369.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.101636 restraints weight = 53495.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101321 restraints weight = 22285.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  12442  Z= 0.299
  Angle     :  0.751   8.089  17413  Z= 0.391
  Chirality :  0.045   0.244   2022
  Planarity :  0.004   0.044   1694
  Dihedral  : 21.196 166.495   3131
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.71 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.25), residues: 1076
  helix: -0.31 (0.22), residues: 531
  sheet: -0.92 (0.51), residues: 104
  loop : -1.23 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  18 
 HIS   0.010   0.002   HIS A 160 
 PHE   0.023   0.002   PHE A1324 
 TYR   0.031   0.002   TYR A 362 
 ARG   0.011   0.001   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07738 (  482)
  hydrogen bonds       : angle       4.84257 ( 1301)
  covalent geometry    : bond        0.00677 (12442)
  covalent geometry    : angle       0.75068 (17413)

*********************** 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: 10
    poor density    : 54
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 10
  residues processed: 62
  average time/residue: 0.3355
  time to fit residues: 29.1384
Evaluate side-chains
  60 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  643 PHE
Chi-restraints excluded: chain A residue  959 LYS
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 1254 GLN
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 109 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.132708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.100095 restraints weight = 22966.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.103130 restraints weight = 47523.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.103097 restraints weight = 21335.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12442  Z= 0.141
  Angle     :  0.592   8.002  17413  Z= 0.312
  Chirality :  0.038   0.225   2022
  Planarity :  0.004   0.053   1694
  Dihedral  : 20.901 171.716   3131
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.33 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.25), residues: 1076
  helix:  0.06 (0.23), residues: 528
  sheet: -0.69 (0.53), residues: 95
  loop : -1.07 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 
 PHE   0.022   0.001   PHE A 196 
 TYR   0.020   0.001   TYR A 362 
 ARG   0.012   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05145 (  482)
  hydrogen bonds       : angle       4.35798 ( 1301)
  covalent geometry    : bond        0.00304 (12442)
  covalent geometry    : angle       0.59186 (17413)

********************** 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
  61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 59
  average time/residue: 0.3083
  time to fit residues: 26.3984
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  : 1.062 
-------------------------------------------------------------------------------
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 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 90 optimal weight:    0.3980
   chunk 85 optimal weight:    0.4980
   chunk 93 optimal weight:    0.0470
   chunk 119 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.5080

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.134300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.102433 restraints weight = 22870.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.104804 restraints weight = 49476.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.105340 restraints weight = 22298.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12442  Z= 0.118
  Angle     :  0.544   7.962  17413  Z= 0.287
  Chirality :  0.036   0.232   2022
  Planarity :  0.003   0.052   1694
  Dihedral  : 20.767 174.559   3131
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 11.53 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1076
  helix:  0.23 (0.23), residues: 529
  sheet: -0.36 (0.56), residues: 92
  loop : -1.03 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 
 PHE   0.038   0.001   PHE A 704 
 TYR   0.017   0.001   TYR A 362 
 ARG   0.012   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04273 (  482)
  hydrogen bonds       : angle       4.10706 ( 1301)
  covalent geometry    : bond        0.00247 (12442)
  covalent geometry    : angle       0.54447 (17413)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3336.40 seconds
wall clock time: 60 minutes 24.27 seconds (3624.27 seconds total)