Starting phenix.real_space_refine
on Thu Sep 18 05:41:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mcc_9067/09_2025/6mcc_9067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mcc_9067/09_2025/6mcc_9067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2025/6mcc_9067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2025/6mcc_9067.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2025/6mcc_9067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2025/6mcc_9067.map"
  }
  resolution = 3.9
  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=   0.005 sd=   0.088
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     118      5.49       5
     S      26      5.16       5
     C    8551      2.51       5
     N    2458      2.21       5
     O    3022      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14175
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 2494
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 115, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1}
            Not linked:
              pdbres="GTP B   1 "
              pdbres="  G B   2 "
    Chain: "A"
      Number of atoms: 10715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1364, 10715
          Classifications: {'peptide': 1364}
          Incomplete info: {'truncation_to_alanine': 104}
          Link IDs: {'PTRANS': 35, 'TRANS': 1328}
          Unresolved non-hydrogen bonds: 441
          Unresolved non-hydrogen angles: 507
          Unresolved non-hydrogen dihedrals: 389
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 20, 'ARG:plan': 12, 'PHE:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 7, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 226
    Chain: "C"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 966
          Classifications: {'peptide': 130}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 126}
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 132
          Unresolved non-hydrogen dihedrals: 84
          Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 6, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 89
  Time building chain proxies: 3.58, per 1000 atoms: 0.25
  Number of scatterers: 14175
  At special positions: 0
  Unit cell: (92, 121.9, 144.9, 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      26     16.00
     P     118     15.00
     O    3022      8.00
     N    2458      7.00
     C    8551      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 552.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2848

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 10 sheets defined
      46.4% alpha, 8.6% beta
      27 base pairs and 56 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 86
      removed outlier: 3.587A  pdb=" N   PHE A  86 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 94
      removed outlier: 3.636A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 102
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 134 through 144
      removed outlier: 4.407A  pdb=" N   ASP A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 160
      removed outlier: 3.583A  pdb=" N   HIS A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 197
      removed outlier: 3.901A  pdb=" N   LEU A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.212A  pdb=" N   ILE A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 5.250A  pdb=" N   GLU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 245
    Processing helix  chain 'A' and resid 270 through 283
      removed outlier: 3.806A  pdb=" N   ASN A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 306
    Processing helix  chain 'A' and resid 317 through 340
      removed outlier: 3.503A  pdb=" N   MET A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 322 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ARG A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ASP A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
      removed outlier: 3.689A  pdb=" N   ILE A 363 " --> pdb=" O   TYR A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.545A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 394
    Processing helix  chain 'A' and resid 411 through 425
      removed outlier: 4.337A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 435
      removed outlier: 3.771A  pdb=" N   ASP A 435 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 474 through 478
      removed outlier: 4.130A  pdb=" N   PHE A 478 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.670A  pdb=" N   GLU A 493 " --> pdb=" O   GLN A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 524
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 604 through 609
      removed outlier: 3.802A  pdb=" N   ASP A 608 " --> pdb=" O   LYS A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.648A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 635
      removed outlier: 4.187A  pdb=" N   GLU A 634 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ARG A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 630 through 635'
    Processing helix  chain 'A' and resid 636 through 640
    Processing helix  chain 'A' and resid 647 through 652
      removed outlier: 3.767A  pdb=" N   LYS A 652 " --> pdb=" O   MET A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 683
    Processing helix  chain 'A' and resid 692 through 699
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 4.540A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ALA A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 725
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 4.280A  pdb=" N   LYS A 749 " --> pdb=" O   ASP A 745 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL A 750 " --> pdb=" O   GLU A 746 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 773
      removed outlier: 3.868A  pdb=" N   LYS A 772 " --> pdb=" O   THR A 769 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLY A 773 " --> pdb=" O   THR A 770 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 769 through 773'
    Processing helix  chain 'A' and resid 774 through 779
      removed outlier: 3.954A  pdb=" N   GLU A 779 " --> pdb=" O   LYS A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 791
      removed outlier: 3.934A  pdb=" N   GLU A 785 " --> pdb=" O   MET A 781 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS A 789 " --> pdb=" O   GLU A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 798
    Processing helix  chain 'A' and resid 808 through 816
    Processing helix  chain 'A' and resid 860 through 864
    Processing helix  chain 'A' and resid 872 through 879
      removed outlier: 3.537A  pdb=" N   MET A 879 " --> pdb=" O   VAL A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 889
      removed outlier: 3.727A  pdb=" N   ARG A 884 " --> pdb=" O   LYS A 880 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN A 885 " --> pdb=" O   ASN A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 901
      removed outlier: 3.796A  pdb=" N   PHE A 897 " --> pdb=" O   THR A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 920
      removed outlier: 3.862A  pdb=" N   GLN A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.613A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   MET A 939 " --> pdb=" O   LEU A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.306A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.591A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASP A 986 " --> pdb=" O   HIS A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1002 through 1006
      removed outlier: 3.941A  pdb=" N   GLU A1005 " --> pdb=" O   PRO A1002 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   SER A1006 " --> pdb=" O   LYS A1003 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1002 through 1006'
    Processing helix  chain 'A' and resid 1041 through 1046
      removed outlier: 3.509A  pdb=" N   ASN A1044 " --> pdb=" O   ASN A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1078
    Processing helix  chain 'A' and resid 1079 through 1088
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 4.188A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1186
    Processing helix  chain 'A' and resid 1191 through 1195
      removed outlier: 3.637A  pdb=" N   ILE A1195 " --> pdb=" O   LYS A1192 " (cutoff:3.500A)
    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 1240
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1263 through 1266
      removed outlier: 3.733A  pdb=" N   LEU A1266 " --> pdb=" O   LYS A1263 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1263 through 1266'
    Processing helix  chain 'A' and resid 1268 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
      removed outlier: 3.695A  pdb=" N   LEU A1287 " --> pdb=" O   ALA A1283 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS A1297 " --> pdb=" O   ALA A1293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1313
    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 1344
      removed outlier: 3.969A  pdb=" N   GLU A1341 " --> pdb=" O   SER A1338 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 19
    Processing helix  chain 'C' and resid 30 through 35
      removed outlier: 3.530A  pdb=" N   LEU C  34 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 3.592A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 5.952A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A1215 " --> pdb=" O   GLU A1219 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509
      removed outlier: 6.408A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.515A  pdb=" N   ALA A 538 " --> pdb=" O   TYR A 529 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1064 through 1065
      removed outlier: 7.548A  pdb=" N   GLU A1064 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A1073 " --> pdb=" O   GLU A1064 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.674A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 72
      removed outlier: 5.830A  pdb=" N   CYS C  70 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLN C  90 " --> pdb=" O   CYS C  70 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ASP C  72 " --> pdb=" O   PHE C  88 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   GLU C  82 " --> pdb=" O   THR C  78 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR C  78 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 72
      removed outlier: 5.830A  pdb=" N   CYS C  70 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLN C  90 " --> pdb=" O   CYS C  70 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ASP C  72 " --> pdb=" O   PHE C  88 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR C  39 " --> pdb=" O   LEU C  89 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS C 127 " --> pdb=" O   ILE C  40 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      66 hydrogen bonds
      128 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      56 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 1.58 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 2348
        1.32 -     1.44: 4340
        1.44 -     1.57: 7714
        1.57 -     1.69: 232
        1.69 -     1.81: 48
  Bond restraints: 14682
  Sorted by residual:
  bond pdb=" C6  GTP B   1 "
       pdb=" O6  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.230  1.387 -0.157 2.00e-02 2.50e+03 6.20e+01
  bond pdb=" C2  GTP B   1 "
       pdb=" N2  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.330  1.426 -0.096 2.00e-02 2.50e+03 2.28e+01
  bond pdb=" C5  GTP B   1 "
       pdb=" C6  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.458 -0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" O3B GTP B   1 "
       pdb=" PB  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.610  1.550  0.060 2.00e-02 2.50e+03 9.00e+00
  bond pdb=" C2  GTP B   1 "
       pdb=" N1  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.380  1.438 -0.058 2.00e-02 2.50e+03 8.37e+00
  ... (remaining 14677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 19768
        2.54 -     5.08: 564
        5.08 -     7.62: 78
        7.62 -    10.16: 18
       10.16 -    12.69: 7
  Bond angle restraints: 20435
  Sorted by residual:
  angle pdb=" C   ASP A 353 "
        pdb=" N   GLN A 354 "
        pdb=" CA  GLN A 354 "
      ideal   model   delta    sigma   weight residual
     121.54  131.86  -10.32 1.91e+00 2.74e-01 2.92e+01
  angle pdb=" C   ASP C 101 "
        pdb=" N   GLU C 102 "
        pdb=" CA  GLU C 102 "
      ideal   model   delta    sigma   weight residual
     121.54  131.54  -10.00 1.91e+00 2.74e-01 2.74e+01
  angle pdb=" CA  THR C 107 "
        pdb=" CB  THR C 107 "
        pdb=" CG2 THR C 107 "
      ideal   model   delta    sigma   weight residual
     110.50  118.04   -7.54 1.70e+00 3.46e-01 1.97e+01
  angle pdb=" N   GLY A1133 "
        pdb=" CA  GLY A1133 "
        pdb=" C   GLY A1133 "
      ideal   model   delta    sigma   weight residual
     110.20  115.93   -5.73 1.32e+00 5.74e-01 1.89e+01
  angle pdb=" C3'   A B  86 "
        pdb=" O3'   A B  86 "
        pdb=" P     A B  87 "
      ideal   model   delta    sigma   weight residual
     120.20  126.65   -6.45 1.50e+00 4.44e-01 1.85e+01
  ... (remaining 20430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.47: 8552
       35.47 -    70.95: 366
       70.95 -   106.42: 39
      106.42 -   141.90: 1
      141.90 -   177.37: 4
  Dihedral angle restraints: 8962
    sinusoidal: 4561
      harmonic: 4401
  Sorted by residual:
  dihedral pdb=" O4'   C B  88 "
           pdb=" C1'   C B  88 "
           pdb=" N1    C B  88 "
           pdb=" C2    C B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.60  159.40     1      1.50e+01 4.44e-03 8.26e+01
  dihedral pdb=" O4'   U B   7 "
           pdb=" C1'   U B   7 "
           pdb=" N1    U B   7 "
           pdb=" C2    U B   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   56.24  175.76     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" CA  THR C 107 "
           pdb=" C   THR C 107 "
           pdb=" N   GLU C 108 "
           pdb=" CA  GLU C 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.35  -34.65     0      5.00e+00 4.00e-02 4.80e+01
  ... (remaining 8959 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.963: 2409
       0.963 -    1.925: 0
       1.925 -    2.888: 0
       2.888 -    3.851: 0
       3.851 -    4.814: 2
  Chirality restraints: 2411
  Sorted by residual:
  chirality pdb=" C2' GTP B   1 "
            pdb=" C1' GTP B   1 "
            pdb=" C3' GTP B   1 "
            pdb=" O2' GTP B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47    2.34   -4.81 2.00e-01 2.50e+01 5.79e+02
  chirality pdb=" C4' GTP B   1 "
            pdb=" C3' GTP B   1 "
            pdb=" C5' GTP B   1 "
            pdb=" O4' GTP B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47    2.25   -4.72 2.00e-01 2.50e+01 5.58e+02
  chirality pdb=" C1'   A B   8 "
            pdb=" O4'   A B   8 "
            pdb=" C2'   A B   8 "
            pdb=" N9    A B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.09    0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 2408 not shown)

  Planarity restraints: 2194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   8 "   -0.035 2.00e-02 2.50e+03   1.80e-02 8.94e+00
        pdb=" N9    A B   8 "    0.047 2.00e-02 2.50e+03
        pdb=" C8    A B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A B   8 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A B   8 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A B   8 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A B   8 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   8 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 302 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.18e+00
        pdb=" C   LEU A 302 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LEU A 302 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER A 303 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 295 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.07e+00
        pdb=" C   ASN A 295 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ASN A 295 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU A 296 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2191 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 4102
        2.81 -     3.33: 12894
        3.33 -     3.86: 24534
        3.86 -     4.38: 26463
        4.38 -     4.90: 42149
  Nonbonded interactions: 110142
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 373 "
            pdb=" O   LEU A 398 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O2'   U B  62 "
            pdb=" OE1 GLN A 402 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG  SER A 469 "
            pdb=" OE1 GLU A 471 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   TYR A 136 "
            pdb=" OG  SER A 318 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   ARG A 925 "
            pdb=" OG1 THR A 928 "
     model   vdw
     2.328 3.040
  ... (remaining 110137 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
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      :  0.006   0.157  14683  Z= 0.304
  Angle     :  1.038  12.694  20435  Z= 0.537
  Chirality :  0.148   4.814   2411
  Planarity :  0.006   0.052   2194
  Dihedral  : 17.836 177.369   6114
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  9.35 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -4.52 (0.17), residues: 1490
  helix: -3.23 (0.14), residues: 609
  sheet: -1.76 (0.45), residues: 111
  loop : -3.02 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A  78 
 TYR   0.023   0.003   TYR A  72 
 PHE   0.044   0.003   PHE A1008 
 TRP   0.042   0.003   TRP A 476 
 HIS   0.009   0.002   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 (14682)
  covalent geometry    : angle       1.03803 (20435)
  hydrogen bonds       : bond        0.17404 (  513)
  hydrogen bonds       : angle       7.67069 ( 1406)
  Misc. bond           : bond        0.04333 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 240
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8879 (p-90) cc_final: 0.8611 (p-90)
REVERT: A  241 LEU cc_start: 0.9103 (mm) cc_final: 0.8611 (pp)
REVERT: A  586 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8452 (mtm-85)
REVERT: A  879 MET cc_start: 0.7602 (mtt) cc_final: 0.7231 (mtt)
REVERT: A  883 TRP cc_start: 0.6278 (m-10) cc_final: 0.5804 (m-10)
REVERT: A 1205 GLU cc_start: 0.8032 (tt0) cc_final: 0.7772 (tt0)
REVERT: C   75 PHE cc_start: 0.8124 (p90) cc_final: 0.7699 (p90)
  outliers start: 13
  outliers final: 3
  residues processed: 249
  average time/residue: 0.1257
  time to fit residues: 45.8792
Evaluate side-chains
  147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  662 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 GLN
A 412 HIS
A 489 GLN
** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN
A 831 ASN
A 930 HIS
A 980 ASN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN
A1054 ASN
A1093 ASN
A1101 GLN
A1297 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.137165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.099084 restraints weight = 29875.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.102011 restraints weight = 15928.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.103018 restraints weight = 10567.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.103378 restraints weight = 8802.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.103501 restraints weight = 8561.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  14683  Z= 0.208
  Angle     :  0.733  13.260  20435  Z= 0.370
  Chirality :  0.043   0.210   2411
  Planarity :  0.005   0.048   2194
  Dihedral  : 19.775 176.863   3378
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 13.23 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -3.29 (0.19), residues: 1490
  helix: -1.75 (0.18), residues: 623
  sheet: -1.50 (0.46), residues: 109
  loop : -2.69 (0.20), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 661 
 TYR   0.020   0.002   TYR A1356 
 PHE   0.033   0.002   PHE A1008 
 TRP   0.019   0.002   TRP A 476 
 HIS   0.006   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (14682)
  covalent geometry    : angle       0.73264 (20435)
  hydrogen bonds       : bond        0.05346 (  513)
  hydrogen bonds       : angle       5.22523 ( 1406)
  Misc. bond           : bond        0.00044 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 168
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8852 (p-90) cc_final: 0.8207 (p-90)
REVERT: A   47 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: A   64 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8408 (tm)
REVERT: A  152 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8108 (ptt90)
REVERT: A  238 PHE cc_start: 0.8257 (t80) cc_final: 0.7879 (t80)
REVERT: A  465 MET cc_start: 0.7826 (ppp) cc_final: 0.7392 (ppp)
REVERT: A  585 ASP cc_start: 0.8122 (p0) cc_final: 0.7627 (p0)
REVERT: A  586 ARG cc_start: 0.8644 (mtm110) cc_final: 0.8430 (mtm-85)
REVERT: A  684 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (tttt)
REVERT: A  706 GLU cc_start: 0.7949 (mp0) cc_final: 0.7699 (mp0)
REVERT: A  761 ILE cc_start: 0.9028 (pp) cc_final: 0.8548 (pp)
REVERT: A  762 GLU cc_start: 0.7495 (pm20) cc_final: 0.7294 (pm20)
REVERT: A  879 MET cc_start: 0.7714 (mtt) cc_final: 0.7163 (mtt)
REVERT: A  957 THR cc_start: 0.8777 (m) cc_final: 0.8570 (p)
REVERT: A 1046 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: A 1089 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8576 (ttt)
REVERT: A 1118 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8055 (tttt)
REVERT: A 1205 GLU cc_start: 0.8190 (tt0) cc_final: 0.7873 (tt0)
REVERT: A 1225 GLU cc_start: 0.8069 (mp0) cc_final: 0.7837 (mp0)
REVERT: A 1365 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8592 (tm)
REVERT: C   25 ARG cc_start: 0.7910 (tmm-80) cc_final: 0.7573 (tmm-80)
REVERT: C   39 TYR cc_start: 0.8651 (m-80) cc_final: 0.8433 (m-10)
REVERT: C  120 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8800 (tp)
  outliers start: 48
  outliers final: 18
  residues processed: 204
  average time/residue: 0.1103
  time to fit residues: 34.3502
Evaluate side-chains
  167 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  684 LYS
Chi-restraints excluded: chain A residue  845 SER
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain A residue 1046 PHE
Chi-restraints excluded: chain A residue 1089 MET
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1365 LEU
Chi-restraints excluded: chain C residue    7 LYS
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 137 optimal weight:    8.9990
   chunk 92 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 132 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9980
   chunk 112 optimal weight:    5.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
A 522 ASN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.134485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.097242 restraints weight = 30159.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.099696 restraints weight = 16173.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.100838 restraints weight = 10885.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.100998 restraints weight = 8867.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.101132 restraints weight = 8753.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14683  Z= 0.220
  Angle     :  0.711  13.610  20435  Z= 0.359
  Chirality :  0.043   0.194   2411
  Planarity :  0.004   0.045   2194
  Dihedral  : 19.668 179.628   3378
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 14.72 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -2.64 (0.20), residues: 1490
  helix: -1.08 (0.19), residues: 633
  sheet: -1.36 (0.46), residues: 113
  loop : -2.45 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  78 
 TYR   0.024   0.002   TYR A 988 
 PHE   0.030   0.002   PHE A1008 
 TRP   0.034   0.002   TRP A 476 
 HIS   0.008   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (14682)
  covalent geometry    : angle       0.71066 (20435)
  hydrogen bonds       : bond        0.05184 (  513)
  hydrogen bonds       : angle       4.98679 ( 1406)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 160
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8894 (p-90) cc_final: 0.8275 (p-90)
REVERT: A   84 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7631 (tp30)
REVERT: A  152 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8233 (ptt90)
REVERT: A  241 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8564 (pp)
REVERT: A  424 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8442 (mmm-85)
REVERT: A  465 MET cc_start: 0.7936 (ppp) cc_final: 0.7665 (ppp)
REVERT: A  585 ASP cc_start: 0.8079 (p0) cc_final: 0.7862 (p0)
REVERT: A  684 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7940 (tttt)
REVERT: A  706 GLU cc_start: 0.7932 (mp0) cc_final: 0.7488 (mp0)
REVERT: A  759 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: A  761 ILE cc_start: 0.9096 (pp) cc_final: 0.8837 (pp)
REVERT: A  879 MET cc_start: 0.7650 (mtt) cc_final: 0.7156 (mtt)
REVERT: A  920 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: A 1021 MET cc_start: 0.8040 (tpp) cc_final: 0.7837 (tpp)
REVERT: A 1046 PHE cc_start: 0.8302 (m-10) cc_final: 0.7853 (m-80)
REVERT: A 1074 TRP cc_start: 0.5101 (t60) cc_final: 0.4728 (t60)
REVERT: A 1089 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8514 (ttt)
REVERT: A 1118 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8100 (tttt)
REVERT: A 1164 LEU cc_start: 0.8783 (tp) cc_final: 0.8515 (tt)
REVERT: A 1205 GLU cc_start: 0.8276 (tt0) cc_final: 0.7943 (tt0)
REVERT: A 1276 PHE cc_start: 0.8423 (t80) cc_final: 0.7936 (t80)
REVERT: A 1296 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8852 (tmmm)
REVERT: A 1313 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7056 (m-10)
REVERT: A 1365 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8673 (tm)
REVERT: C   97 ASP cc_start: 0.8189 (t0) cc_final: 0.7350 (p0)
REVERT: C  120 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8844 (tp)
  outliers start: 63
  outliers final: 31
  residues processed: 203
  average time/residue: 0.1068
  time to fit residues: 33.5807
Evaluate side-chains
  180 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  684 LYS
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue  845 SER
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain A residue 1089 MET
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1144 LEU
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1296 LYS
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1365 LEU
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 151 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0980
   chunk 91 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9980
   chunk 135 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 137 HIS
A 224 ASN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.139867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.102262 restraints weight = 29537.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.105328 restraints weight = 16141.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.106408 restraints weight = 10055.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.106918 restraints weight = 8253.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.106960 restraints weight = 7961.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14683  Z= 0.111
  Angle     :  0.634  14.723  20435  Z= 0.306
  Chirality :  0.039   0.216   2411
  Planarity :  0.003   0.041   2194
  Dihedral  : 19.500 174.802   3378
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 16.54 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -2.03 (0.21), residues: 1490
  helix: -0.44 (0.20), residues: 626
  sheet: -1.16 (0.46), residues: 113
  loop : -2.21 (0.21), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 221 
 TYR   0.024   0.001   TYR A 988 
 PHE   0.030   0.001   PHE A1008 
 TRP   0.017   0.002   TRP A 476 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (14682)
  covalent geometry    : angle       0.63355 (20435)
  hydrogen bonds       : bond        0.04073 (  513)
  hydrogen bonds       : angle       4.53328 ( 1406)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 176
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8795 (p-90) cc_final: 0.8132 (p-90)
REVERT: A  241 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8525 (pp)
REVERT: A  465 MET cc_start: 0.7603 (ppp) cc_final: 0.7256 (ptm)
REVERT: A  585 ASP cc_start: 0.7940 (p0) cc_final: 0.7725 (p0)
REVERT: A  706 GLU cc_start: 0.7828 (mp0) cc_final: 0.7335 (mp0)
REVERT: A  761 ILE cc_start: 0.9126 (pp) cc_final: 0.8773 (pp)
REVERT: A  883 TRP cc_start: 0.5826 (m-10) cc_final: 0.5551 (m-90)
REVERT: A  920 GLN cc_start: 0.8276 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: A 1021 MET cc_start: 0.7863 (tpp) cc_final: 0.7611 (tpp)
REVERT: A 1046 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7690 (m-80)
REVERT: A 1074 TRP cc_start: 0.4668 (t60) cc_final: 0.4401 (t60)
REVERT: A 1205 GLU cc_start: 0.8121 (tt0) cc_final: 0.7763 (tt0)
REVERT: A 1313 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6790 (m-10)
REVERT: A 1337 THR cc_start: 0.8287 (p) cc_final: 0.8065 (p)
REVERT: A 1365 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8588 (tm)
REVERT: C  120 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8872 (tp)
  outliers start: 48
  outliers final: 22
  residues processed: 208
  average time/residue: 0.1058
  time to fit residues: 34.2660
Evaluate side-chains
  174 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue 1046 PHE
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1365 LEU
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 88 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   chunk 136 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 37 optimal weight:    0.4980
   chunk 117 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.138413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.100017 restraints weight = 31029.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.102578 restraints weight = 16593.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.103867 restraints weight = 11079.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.104304 restraints weight = 9008.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.104412 restraints weight = 8708.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14683  Z= 0.147
  Angle     :  0.642  13.958  20435  Z= 0.315
  Chirality :  0.040   0.228   2411
  Planarity :  0.003   0.043   2194
  Dihedral  : 19.429 174.964   3378
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.53 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.81 (0.21), residues: 1490
  helix: -0.21 (0.21), residues: 627
  sheet: -1.15 (0.46), residues: 113
  loop : -2.11 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  78 
 TYR   0.022   0.001   TYR A 988 
 PHE   0.029   0.001   PHE A1008 
 TRP   0.018   0.002   TRP A 476 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (14682)
  covalent geometry    : angle       0.64237 (20435)
  hydrogen bonds       : bond        0.04439 (  513)
  hydrogen bonds       : angle       4.52936 ( 1406)
  Misc. bond           : bond        0.00032 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 163
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8810 (p-90) cc_final: 0.7902 (p-90)
REVERT: A  152 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8551 (ptt90)
REVERT: A  241 LEU cc_start: 0.9072 (mm) cc_final: 0.8554 (pp)
REVERT: A  465 MET cc_start: 0.7910 (ppp) cc_final: 0.7475 (ptm)
REVERT: A  585 ASP cc_start: 0.7972 (p0) cc_final: 0.7670 (p0)
REVERT: A  786 GLU cc_start: 0.8649 (tp30) cc_final: 0.8431 (tp30)
REVERT: A  920 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7960 (tm-30)
REVERT: A 1021 MET cc_start: 0.7782 (tpp) cc_final: 0.7554 (tpp)
REVERT: A 1043 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8344 (tpp)
REVERT: A 1046 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7659 (m-80)
REVERT: A 1205 GLU cc_start: 0.8168 (tt0) cc_final: 0.7813 (tt0)
REVERT: A 1296 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8719 (tmmm)
REVERT: A 1313 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7056 (m-10)
REVERT: C   25 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8843 (mmm160)
REVERT: C  120 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8921 (tp)
  outliers start: 49
  outliers final: 30
  residues processed: 199
  average time/residue: 0.1107
  time to fit residues: 34.2179
Evaluate side-chains
  176 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain A residue 1043 MET
Chi-restraints excluded: chain A residue 1046 PHE
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1144 LEU
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1296 LYS
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   chunk 127 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 135 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 158 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0770
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.8146

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

Flipped N/Q/H residues before XYZ refinement:
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.134420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100054 restraints weight = 29430.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.101758 restraints weight = 16301.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.102465 restraints weight = 11634.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.102847 restraints weight = 10084.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.103197 restraints weight = 9222.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14683  Z= 0.178
  Angle     :  0.664  13.242  20435  Z= 0.329
  Chirality :  0.041   0.177   2411
  Planarity :  0.003   0.042   2194
  Dihedral  : 19.407 174.788   3378
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 18.20 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.69 (0.21), residues: 1490
  helix: -0.10 (0.21), residues: 627
  sheet: -1.18 (0.48), residues: 113
  loop : -2.05 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  78 
 TYR   0.022   0.002   TYR A 988 
 PHE   0.027   0.002   PHE A1008 
 TRP   0.033   0.004   TRP A1074 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (14682)
  covalent geometry    : angle       0.66415 (20435)
  hydrogen bonds       : bond        0.04629 (  513)
  hydrogen bonds       : angle       4.57621 ( 1406)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 149
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8749 (p-90) cc_final: 0.7939 (p-90)
REVERT: A   47 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7586 (tt)
REVERT: A  152 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8602 (ptt90)
REVERT: A  241 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8574 (pp)
REVERT: A  465 MET cc_start: 0.7845 (ppp) cc_final: 0.7382 (ptm)
REVERT: A  585 ASP cc_start: 0.7779 (p0) cc_final: 0.7428 (p0)
REVERT: A  712 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7743 (mm110)
REVERT: A 1089 MET cc_start: 0.8591 (ttt) cc_final: 0.8170 (ttt)
REVERT: A 1164 LEU cc_start: 0.8870 (tp) cc_final: 0.8610 (tt)
REVERT: A 1205 GLU cc_start: 0.8104 (tt0) cc_final: 0.7794 (tt0)
REVERT: A 1313 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6980 (m-10)
REVERT: C    7 LYS cc_start: 0.8536 (ptmm) cc_final: 0.8225 (ptmm)
REVERT: C   97 ASP cc_start: 0.8016 (t0) cc_final: 0.7398 (t0)
REVERT: C  120 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8879 (tp)
  outliers start: 59
  outliers final: 40
  residues processed: 188
  average time/residue: 0.1078
  time to fit residues: 31.5046
Evaluate side-chains
  188 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 142
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  639 TYR
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 124 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1297 HIS

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 = 0.133168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.094720 restraints weight = 30305.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.098082 restraints weight = 16120.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.100323 restraints weight = 10907.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.101755 restraints weight = 8553.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.102620 restraints weight = 7360.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14683  Z= 0.177
  Angle     :  0.670  13.527  20435  Z= 0.330
  Chirality :  0.041   0.174   2411
  Planarity :  0.003   0.041   2194
  Dihedral  : 19.377 174.779   3378
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 18.61 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.59 (0.22), residues: 1490
  helix: -0.02 (0.21), residues: 627
  sheet: -1.13 (0.48), residues: 115
  loop : -1.99 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  25 
 TYR   0.023   0.002   TYR A 988 
 PHE   0.026   0.002   PHE A 916 
 TRP   0.019   0.003   TRP A 883 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (14682)
  covalent geometry    : angle       0.66990 (20435)
  hydrogen bonds       : bond        0.04641 (  513)
  hydrogen bonds       : angle       4.57426 ( 1406)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 153
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7993 (tt)
REVERT: A  241 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8642 (pp)
REVERT: A  383 MET cc_start: 0.7989 (mmp) cc_final: 0.7549 (mmm)
REVERT: A  465 MET cc_start: 0.7950 (ppp) cc_final: 0.7464 (ptm)
REVERT: A  585 ASP cc_start: 0.7688 (p0) cc_final: 0.7337 (p0)
REVERT: A  712 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7791 (mm110)
REVERT: A  761 ILE cc_start: 0.9115 (pp) cc_final: 0.8815 (pp)
REVERT: A  916 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (t80)
REVERT: A  920 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: A 1021 MET cc_start: 0.7528 (tpp) cc_final: 0.6937 (tpp)
REVERT: A 1205 GLU cc_start: 0.8147 (tt0) cc_final: 0.7807 (tt0)
REVERT: A 1313 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6961 (m-10)
REVERT: C   96 GLU cc_start: 0.8551 (tp30) cc_final: 0.8261 (tm-30)
REVERT: C   97 ASP cc_start: 0.8000 (t0) cc_final: 0.7485 (t0)
REVERT: C  120 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8898 (tp)
  outliers start: 64
  outliers final: 39
  residues processed: 196
  average time/residue: 0.1090
  time to fit residues: 33.0626
Evaluate side-chains
  186 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 141
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  639 TYR
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1311 HIS
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 91 optimal weight:   30.0000
   chunk 69 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   chunk 147 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 109 optimal weight:    0.6980
   chunk 133 optimal weight:    4.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 818 ASN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.130970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.092396 restraints weight = 30605.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.095698 restraints weight = 16346.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.097863 restraints weight = 11131.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.099213 restraints weight = 8785.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.100045 restraints weight = 7598.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14683  Z= 0.234
  Angle     :  0.732  13.239  20435  Z= 0.364
  Chirality :  0.044   0.269   2411
  Planarity :  0.004   0.043   2194
  Dihedral  : 19.420 174.306   3378
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 20.10 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.73 (0.21), residues: 1490
  helix: -0.12 (0.21), residues: 619
  sheet: -1.31 (0.47), residues: 115
  loop : -2.04 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  25 
 TYR   0.024   0.002   TYR A 988 
 PHE   0.041   0.002   PHE A 916 
 TRP   0.057   0.004   TRP A1074 
 HIS   0.006   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (14682)
  covalent geometry    : angle       0.73202 (20435)
  hydrogen bonds       : bond        0.05187 (  513)
  hydrogen bonds       : angle       4.78586 ( 1406)
  Misc. bond           : bond        0.00073 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 145
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A  241 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8658 (pp)
REVERT: A  383 MET cc_start: 0.8256 (mmp) cc_final: 0.7945 (mmm)
REVERT: A  465 MET cc_start: 0.7957 (ppp) cc_final: 0.7519 (ptm)
REVERT: A  585 ASP cc_start: 0.7807 (p0) cc_final: 0.7442 (p0)
REVERT: A  712 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7877 (mm110)
REVERT: A  916 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7817 (t80)
REVERT: A 1000 LYS cc_start: 0.8674 (tmtt) cc_final: 0.8258 (tptt)
REVERT: A 1021 MET cc_start: 0.7767 (tpp) cc_final: 0.7151 (tpp)
REVERT: A 1205 GLU cc_start: 0.8182 (tt0) cc_final: 0.7851 (tt0)
REVERT: A 1313 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7070 (m-10)
REVERT: C   96 GLU cc_start: 0.8591 (tp30) cc_final: 0.8316 (tm-30)
REVERT: C   97 ASP cc_start: 0.8163 (t0) cc_final: 0.7682 (t0)
REVERT: C  100 GLU cc_start: 0.8379 (mp0) cc_final: 0.8160 (pm20)
  outliers start: 57
  outliers final: 38
  residues processed: 185
  average time/residue: 0.1030
  time to fit residues: 29.9977
Evaluate side-chains
  186 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 144
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1144 LEU
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1311 HIS
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  127 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 158 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 140 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 3 optimal weight:   20.0000
   chunk 110 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.134060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.095942 restraints weight = 30163.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.099339 restraints weight = 16018.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.101553 restraints weight = 10851.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.103010 restraints weight = 8477.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.103830 restraints weight = 7275.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14683  Z= 0.149
  Angle     :  0.680  16.316  20435  Z= 0.331
  Chirality :  0.041   0.284   2411
  Planarity :  0.003   0.040   2194
  Dihedral  : 19.282 175.282   3378
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 20.76 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.52 (0.22), residues: 1490
  helix:  0.07 (0.21), residues: 623
  sheet: -1.24 (0.48), residues: 115
  loop : -1.95 (0.22), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  25 
 TYR   0.021   0.001   TYR A 988 
 PHE   0.028   0.001   PHE A 916 
 TRP   0.034   0.003   TRP A1074 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (14682)
  covalent geometry    : angle       0.68022 (20435)
  hydrogen bonds       : bond        0.04413 (  513)
  hydrogen bonds       : angle       4.52461 ( 1406)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 156
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8701 (pp)
REVERT: A  383 MET cc_start: 0.8316 (mmp) cc_final: 0.7914 (mmm)
REVERT: A  396 GLU cc_start: 0.8500 (tp30) cc_final: 0.8116 (tp30)
REVERT: A  465 MET cc_start: 0.7869 (ppp) cc_final: 0.7423 (ptm)
REVERT: A  585 ASP cc_start: 0.7770 (p0) cc_final: 0.7421 (p0)
REVERT: A  712 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7805 (mm110)
REVERT: A 1021 MET cc_start: 0.7588 (tpp) cc_final: 0.7271 (tpp)
REVERT: A 1089 MET cc_start: 0.8599 (mmm) cc_final: 0.7989 (ttt)
REVERT: A 1205 GLU cc_start: 0.8145 (tt0) cc_final: 0.7814 (tt0)
REVERT: A 1313 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6852 (m-10)
REVERT: C   96 GLU cc_start: 0.8547 (tp30) cc_final: 0.8327 (tm-30)
REVERT: C   97 ASP cc_start: 0.8087 (t0) cc_final: 0.7652 (t0)
  outliers start: 48
  outliers final: 34
  residues processed: 189
  average time/residue: 0.1047
  time to fit residues: 30.9988
Evaluate side-chains
  182 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1144 LEU
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1311 HIS
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   95 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0670
   chunk 147 optimal weight:    2.9990
   chunk 140 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.1120

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 ASN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.138714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.100201 restraints weight = 29285.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.103732 restraints weight = 15063.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.106141 restraints weight = 10029.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.107621 restraints weight = 7742.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108664 restraints weight = 6609.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14683  Z= 0.120
  Angle     :  0.670  16.703  20435  Z= 0.322
  Chirality :  0.039   0.264   2411
  Planarity :  0.003   0.041   2194
  Dihedral  : 19.149 176.890   3378
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.59 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.35 (0.22), residues: 1490
  helix:  0.23 (0.21), residues: 630
  sheet: -1.24 (0.48), residues: 115
  loop : -1.87 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  25 
 TYR   0.022   0.001   TYR A 988 
 PHE   0.036   0.001   PHE A1008 
 TRP   0.024   0.002   TRP A1074 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (14682)
  covalent geometry    : angle       0.66980 (20435)
  hydrogen bonds       : bond        0.03993 (  513)
  hydrogen bonds       : angle       4.35714 ( 1406)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8698 (pp)
REVERT: A  396 GLU cc_start: 0.8501 (tp30) cc_final: 0.8296 (tp30)
REVERT: A  465 MET cc_start: 0.7843 (ppp) cc_final: 0.7376 (ptm)
REVERT: A  585 ASP cc_start: 0.7792 (p0) cc_final: 0.7459 (p0)
REVERT: A  618 ASP cc_start: 0.8732 (p0) cc_final: 0.8312 (p0)
REVERT: A  712 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7932 (mm110)
REVERT: A  762 GLU cc_start: 0.6908 (pm20) cc_final: 0.6486 (pm20)
REVERT: A 1021 MET cc_start: 0.7399 (tpp) cc_final: 0.7093 (tpp)
REVERT: A 1045 PHE cc_start: 0.9033 (t80) cc_final: 0.8722 (t80)
REVERT: A 1089 MET cc_start: 0.8643 (mmm) cc_final: 0.8108 (ttt)
REVERT: A 1313 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6838 (m-10)
REVERT: C   35 ASN cc_start: 0.8818 (m110) cc_final: 0.8605 (m-40)
REVERT: C   96 GLU cc_start: 0.8605 (tp30) cc_final: 0.8293 (tm-30)
REVERT: C   97 ASP cc_start: 0.8071 (t0) cc_final: 0.7672 (t0)
  outliers start: 40
  outliers final: 27
  residues processed: 184
  average time/residue: 0.1006
  time to fit residues: 29.2760
Evaluate side-chains
  177 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LYS
Chi-restraints excluded: chain A residue 1144 LEU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1311 HIS
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   95 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 99 optimal weight:   10.0000
   chunk 152 optimal weight:    0.0060
   chunk 6 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 156 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 97 optimal weight:    0.2980
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.6602

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.136838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.098306 restraints weight = 29418.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.101832 restraints weight = 15274.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.104139 restraints weight = 10202.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.105637 restraints weight = 7926.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.106585 restraints weight = 6776.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14683  Z= 0.137
  Angle     :  0.683  16.655  20435  Z= 0.331
  Chirality :  0.040   0.251   2411
  Planarity :  0.003   0.040   2194
  Dihedral  : 19.076 176.947   3378
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.75 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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 aren not related in a simple way.
  whole: -1.26 (0.22), residues: 1490
  helix:  0.30 (0.22), residues: 624
  sheet: -0.81 (0.52), residues: 95
  loop : -1.86 (0.22), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  25 
 TYR   0.022   0.001   TYR A 988 
 PHE   0.041   0.001   PHE A 916 
 TRP   0.026   0.002   TRP A1074 
 HIS   0.019   0.001   HIS A 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (14682)
  covalent geometry    : angle       0.68310 (20435)
  hydrogen bonds       : bond        0.04257 (  513)
  hydrogen bonds       : angle       4.42859 ( 1406)
  Misc. bond           : bond        0.00046 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2311.50 seconds
wall clock time: 40 minutes 54.11 seconds (2454.11 seconds total)