Starting phenix.real_space_refine
on Thu Sep 18 05:28:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5vzl_8749/09_2025/5vzl_8749_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5vzl_8749/09_2025/5vzl_8749.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2025/5vzl_8749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2025/5vzl_8749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2025/5vzl_8749_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2025/5vzl_8749_neut.cif"
  }
  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=   0.000 sd=   0.005
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      25      5.16       5
     C    8364      2.51       5
     N    2420      2.21       5
     O    2988      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: 13915
  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: 10711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1364, 10711
          Classifications: {'peptide': 1364}
          Incomplete info: {'truncation_to_alanine': 106}
          Link IDs: {'PTRANS': 35, 'TRANS': 1328}
          Unresolved non-hydrogen bonds: 445
          Unresolved non-hydrogen angles: 510
          Unresolved non-hydrogen dihedrals: 394
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 21, 'ARG:plan': 10, 'PHE:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 7, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 220
    Chain: "C"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 710
          Classifications: {'peptide': 87}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 3.36, per 1000 atoms: 0.24
  Number of scatterers: 13915
  At special positions: 0
  Unit cell: (112.35, 136.96, 120.91, 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      25     16.00
     P     118     15.00
     O    2988      8.00
     N    2420      7.00
     C    8364      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: 1.18
  Conformation dependent library (CDL) restraints added in 564.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2760

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 11 sheets defined
      52.0% alpha, 6.6% beta
      30 base pairs and 57 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 86
      removed outlier: 3.556A  pdb=" N   ARG A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 94
      removed outlier: 3.739A  pdb=" N   MET A  90 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 135 through 144
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.866A  pdb=" N   LYS A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 197
      removed outlier: 3.768A  pdb=" N   LEU A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 214
      removed outlier: 3.807A  pdb=" N   ALA A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.865A  pdb=" N   GLU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN A 224 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.859A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
      removed outlier: 5.253A  pdb=" N   ASP A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 282
      No H-bonds generated for 'chain 'A' and resid 281 through 282'
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 286 through 306
    Processing helix  chain 'A' and resid 317 through 343
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.506A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.816A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.314A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 422 " --> pdb=" O   GLU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
      removed outlier: 3.709A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 445
    Processing helix  chain 'A' and resid 477 through 481
      removed outlier: 3.632A  pdb=" N   VAL A 481 " --> pdb=" O   PHE A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 496
    Processing helix  chain 'A' and resid 512 through 525
    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 603 through 608
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 635
      removed outlier: 3.904A  pdb=" N   ARG A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 652
      removed outlier: 4.328A  pdb=" N   LYS A 652 " --> pdb=" O   MET A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 668
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 713
      removed outlier: 3.860A  pdb=" N   ALA A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
      removed outlier: 3.579A  pdb=" N   HIS A 723 " --> pdb=" O   SER A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 751
    Processing helix  chain 'A' and resid 769 through 773
      removed outlier: 3.898A  pdb=" N   LYS A 772 " --> pdb=" O   THR A 769 " (cutoff:3.500A)
      removed outlier: 3.976A  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 776 through 792
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 3.620A  pdb=" N   LYS A 797 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 817
      removed outlier: 3.613A  pdb=" N   TYR A 812 " --> pdb=" O   ASN A 808 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLN A 817 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 864
      removed outlier: 3.593A  pdb=" N   ARG A 864 " --> pdb=" O   ASP A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 877
      removed outlier: 3.708A  pdb=" N   LYS A 877 " --> pdb=" O   GLU A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 889
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 902 through 906
    Processing helix  chain 'A' and resid 909 through 921
      removed outlier: 3.834A  pdb=" N   GLN A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.592A  pdb=" N   ARG A 938 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   MET A 939 " --> pdb=" O   LEU A 935 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 3.822A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1001
    Processing helix  chain 'A' and resid 1004 through 1008
      removed outlier: 3.767A  pdb=" N   GLU A1007 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1022
    Processing helix  chain 'A' and resid 1043 through 1047
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1186
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
      removed outlier: 3.850A  pdb=" N   HIS A1262 " --> pdb=" O   PHE A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1263 through 1281
      removed outlier: 3.974A  pdb=" N   ASP A1267 " --> pdb=" O   LYS A1263 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ARG A1279 " --> pdb=" O   GLU A1275 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL A1280 " --> pdb=" O   PHE A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
      removed outlier: 3.609A  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 1317
    Processing helix  chain 'A' and resid 1339 through 1344
      removed outlier: 3.627A  pdb=" N   LEU A1343 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 13
      removed outlier: 3.934A  pdb=" N   LEU C   6 " --> pdb=" O   ASN C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 59
    Processing helix  chain 'C' and resid 70 through 83
      removed outlier: 3.999A  pdb=" N   LEU C  82 " --> pdb=" O   GLN C  78 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS C  83 " --> pdb=" O   THR C  79 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 3.597A  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: 6.178A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1050 through 1051
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065
      removed outlier: 6.267A  pdb=" N   GLU A1064 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.564A  pdb=" N   GLU A1162 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL A1145 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE A1166 " --> pdb=" O   TYR A1141 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325
      removed outlier: 3.796A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31
      removed outlier: 3.938A  pdb=" N   ILE C  43 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)

    495 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      57 stacking parallelities
  Total time for adding SS restraints: 3.16

  Time building geometry restraints manager: 1.60 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: 2283
        1.32 -     1.44: 4269
        1.44 -     1.56: 7579
        1.56 -     1.69: 234
        1.69 -     1.81: 48
  Bond restraints: 14413
  Sorted by residual:
  bond pdb=" C3'   A B  47 "
       pdb=" O3'   A B  47 "
    ideal  model  delta    sigma   weight residual
    1.427  1.453 -0.026 1.50e-02 4.44e+03 2.90e+00
  bond pdb=" C   GLY A1319 "
       pdb=" N   ALA A1320 "
    ideal  model  delta    sigma   weight residual
    1.340  1.243  0.098 5.87e-02 2.90e+02 2.77e+00
  bond pdb=" N9    G B   4 "
       pdb=" C4    G B   4 "
    ideal  model  delta    sigma   weight residual
    1.375  1.405 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" C   LEU A 229 "
       pdb=" N   PRO A 230 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 2.03e+00
  bond pdb=" CB  PHE A 972 "
       pdb=" CG  PHE A 972 "
    ideal  model  delta    sigma   weight residual
    1.502  1.470  0.032 2.30e-02 1.89e+03 1.97e+00
  ... (remaining 14408 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 19515
        2.48 -     4.96: 462
        4.96 -     7.43: 65
        7.43 -     9.91: 14
        9.91 -    12.39: 3
  Bond angle restraints: 20059
  Sorted by residual:
  angle pdb=" N   VAL A1015 "
        pdb=" CA  VAL A1015 "
        pdb=" C   VAL A1015 "
      ideal   model   delta    sigma   weight residual
     111.91  106.73    5.18 8.90e-01 1.26e+00 3.38e+01
  angle pdb=" C3'   A B  47 "
        pdb=" O3'   A B  47 "
        pdb=" P     A B  48 "
      ideal   model   delta    sigma   weight residual
     120.20  127.23   -7.03 1.50e+00 4.44e-01 2.20e+01
  angle pdb=" CA  ARG C  33 "
        pdb=" CB  ARG C  33 "
        pdb=" CG  ARG C  33 "
      ideal   model   delta    sigma   weight residual
     114.10  123.27   -9.17 2.00e+00 2.50e-01 2.10e+01
  angle pdb=" C   PHE A 196 "
        pdb=" N   GLU A 197 "
        pdb=" CA  GLU A 197 "
      ideal   model   delta    sigma   weight residual
     121.54  129.92   -8.38 1.91e+00 2.74e-01 1.93e+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  126.54   -6.34 1.50e+00 4.44e-01 1.79e+01
  ... (remaining 20054 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.20: 8449
       35.20 -    70.39: 317
       70.39 -   105.59: 37
      105.59 -   140.78: 4
      140.78 -   175.98: 5
  Dihedral angle restraints: 8812
    sinusoidal: 4546
      harmonic: 4266
  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   39.82  160.18     1      1.50e+01 4.44e-03 8.28e+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   56.02  175.98     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  SER C  46 "
           pdb=" C   SER C  46 "
           pdb=" N   GLU C  47 "
           pdb=" CA  GLU C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.46   36.54     0      5.00e+00 4.00e-02 5.34e+01
  ... (remaining 8809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1930
       0.062 -    0.125: 377
       0.125 -    0.187: 39
       0.187 -    0.250: 8
       0.250 -    0.312: 2
  Chirality restraints: 2356
  Sorted by residual:
  chirality pdb=" C3'   C B  35 "
            pdb=" C4'   C B  35 "
            pdb=" O3'   C B  35 "
            pdb=" C2'   C B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.17   -0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" C3'   A B  47 "
            pdb=" C4'   A B  47 "
            pdb=" O3'   A B  47 "
            pdb=" C2'   A B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.49   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" P     A B  48 "
            pdb=" OP1   A B  48 "
            pdb=" OP2   A B  48 "
            pdb=" O5'   A B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.64   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 2353 not shown)

  Planarity restraints: 2153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  47 "    0.040 2.00e-02 2.50e+03   1.79e-02 8.80e+00
        pdb=" N9    A B  47 "   -0.038 2.00e-02 2.50e+03
        pdb=" C8    A B  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    A B  47 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A B  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B  47 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A B  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A B  47 "    0.013 2.00e-02 2.50e+03
        pdb=" C2    A B  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    A B  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4    A B  47 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 271 "    0.014 2.00e-02 2.50e+03   2.90e-02 8.39e+00
        pdb=" C   TYR A 271 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   TYR A 271 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP A 272 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1326 "    0.014 2.00e-02 2.50e+03   2.83e-02 7.98e+00
        pdb=" C   TYR A1326 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   TYR A1326 "    0.018 2.00e-02 2.50e+03
        pdb=" N   PHE A1327 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2150 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 2067
        2.75 -     3.29: 13382
        3.29 -     3.83: 24507
        3.83 -     4.36: 27918
        4.36 -     4.90: 42797
  Nonbonded interactions: 110671
  Sorted by model distance:
  nonbonded pdb=" O2'   G B  61 "
            pdb=" OH  TYR A 359 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   GLN C  78 "
            pdb=" OG1 THR C  81 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OH  TYR A   5 "
            pdb=" O   HIS A 754 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG1 THR A 474 "
            pdb=" OD1 ASN A 477 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG1 THR A 560 "
            pdb=" OD1 ASP A 585 "
     model   vdw
     2.296 3.040
  ... (remaining 110666 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.090
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0248
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   0.098  14414  Z= 0.285
  Angle     :  0.958  12.390  20059  Z= 0.508
  Chirality :  0.050   0.312   2356
  Planarity :  0.006   0.068   2153
  Dihedral  : 17.273 175.978   6052
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  3.33 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -4.13 (0.17), residues: 1447
  helix: -2.93 (0.14), residues: 661
  sheet: -1.64 (0.49), residues: 110
  loop : -2.64 (0.21), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  78 
 TYR   0.028   0.003   TYR A 973 
 PHE   0.020   0.003   PHE A1008 
 TRP   0.011   0.003   TRP A 464 
 HIS   0.007   0.002   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 (14413)
  covalent geometry    : angle       0.95819 (20059)
  hydrogen bonds       : bond        0.15738 (  567)
  hydrogen bonds       : angle       9.97298 ( 1540)
  Misc. bond           : bond        0.00028 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ARG cc_start: -0.3469 (OUTLIER) cc_final: -0.3745 (mpt-90)
REVERT: A  642 LEU cc_start: 0.3241 (mm) cc_final: 0.2945 (mm)
REVERT: A  643 PHE cc_start: 0.0746 (m-10) cc_final: 0.0429 (m-80)
REVERT: A  822 MET cc_start: -0.4326 (mmm) cc_final: -0.5093 (mtt)
REVERT: A 1213 MET cc_start: 0.4589 (mtm) cc_final: 0.4065 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1536
  time to fit residues: 26.8052
Evaluate side-chains
  82 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.3980
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
A 137 HIS
A 194 GLN
A 420 HIS
A 501 ASN
A 522 ASN
A 595 HIS
A 709 GLN
A 767 ASN
A 807 GLN
A 863 ASN
A1091 GLN
A1286 ASN
C   2 ASN
C  12 ASN
C  25 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5045 r_free = 0.5045 target = 0.264967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.225597 restraints weight = 29529.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.230798 restraints weight = 16098.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4865 r_free = 0.4865 target = 0.234283 restraints weight = 10306.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.236620 restraints weight = 7510.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.237904 restraints weight = 6030.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0585
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14414  Z= 0.152
  Angle     :  0.621   9.439  20059  Z= 0.323
  Chirality :  0.039   0.247   2356
  Planarity :  0.005   0.068   2153
  Dihedral  : 19.983 179.180   3330
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  6.42 %
    Favored  : 92.33 %
  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: -2.37 (0.20), residues: 1447
  helix: -0.84 (0.18), residues: 681
  sheet: -1.93 (0.41), residues: 135
  loop : -2.27 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1333 
 TYR   0.019   0.002   TYR A 155 
 PHE   0.012   0.002   PHE A 693 
 TRP   0.009   0.001   TRP A 476 
 HIS   0.009   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (14413)
  covalent geometry    : angle       0.62102 (20059)
  hydrogen bonds       : bond        0.04069 (  567)
  hydrogen bonds       : angle       5.45885 ( 1540)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 PHE cc_start: -0.0384 (m-10) cc_final: -0.1381 (m-10)
REVERT: A  161 MET cc_start: 0.1701 (mmm) cc_final: 0.1404 (mmm)
REVERT: A  194 GLN cc_start: -0.2487 (OUTLIER) cc_final: -0.3435 (mm-40)
REVERT: A  207 ASP cc_start: 0.5560 (t0) cc_final: 0.5275 (p0)
REVERT: A  241 LEU cc_start: -0.1786 (OUTLIER) cc_final: -0.2546 (mp)
REVERT: A  694 MET cc_start: -0.1021 (ppp) cc_final: -0.3017 (mtm)
REVERT: A  822 MET cc_start: -0.2807 (mmm) cc_final: -0.4205 (mtt)
  outliers start: 15
  outliers final: 5
  residues processed: 105
  average time/residue: 0.1250
  time to fit residues: 19.3346
Evaluate side-chains
  82 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain C residue   28 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 139 optimal weight:    0.6980
   chunk 146 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
A 817 GLN
A 920 GLN
** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1241 HIS
A1264 HIS
A1308 ASN
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.267503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.228770 restraints weight = 29445.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.233700 restraints weight = 15719.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4919 r_free = 0.4919 target = 0.236914 restraints weight = 9950.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4937 r_free = 0.4937 target = 0.238912 restraints weight = 7216.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.240364 restraints weight = 5837.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.4865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1194
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14414  Z= 0.176
  Angle     :  0.712  10.033  20059  Z= 0.368
  Chirality :  0.042   0.244   2356
  Planarity :  0.005   0.069   2153
  Dihedral  : 19.791 177.687   3326
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  8.25 %
    Favored  : 89.33 %
  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: -1.89 (0.20), residues: 1447
  helix: -0.39 (0.18), residues: 696
  sheet: -0.83 (0.49), residues: 93
  loop : -2.30 (0.21), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 557 
 TYR   0.020   0.002   TYR A 656 
 PHE   0.024   0.003   PHE C  73 
 TRP   0.018   0.002   TRP A 476 
 HIS   0.013   0.002   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (14413)
  covalent geometry    : angle       0.71234 (20059)
  hydrogen bonds       : bond        0.04861 (  567)
  hydrogen bonds       : angle       5.21943 ( 1540)
  Misc. bond           : bond        0.00045 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.3625 (OUTLIER) cc_final: 0.3395 (m-10)
REVERT: A  161 MET cc_start: 0.2162 (mmm) cc_final: 0.1611 (mmm)
REVERT: A  241 LEU cc_start: -0.1836 (OUTLIER) cc_final: -0.2482 (mp)
REVERT: A  684 LYS cc_start: 0.7306 (mtmt) cc_final: 0.7065 (mtmm)
REVERT: A  904 GLU cc_start: 0.5340 (tt0) cc_final: 0.4031 (mt-10)
REVERT: A  970 PHE cc_start: 0.2102 (m-80) cc_final: 0.0584 (m-80)
REVERT: A 1060 ARG cc_start: 0.3303 (mtp85) cc_final: 0.2392 (mmm160)
REVERT: A 1089 MET cc_start: 0.1314 (tmm) cc_final: 0.0767 (tmm)
REVERT: C   30 LEU cc_start: -0.2171 (OUTLIER) cc_final: -0.2862 (tp)
REVERT: C   77 MET cc_start: -0.0139 (mmp) cc_final: -0.1396 (ptt)
REVERT: C   80 ILE cc_start: -0.2555 (OUTLIER) cc_final: -0.3986 (pt)
  outliers start: 29
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1343
  time to fit residues: 22.6717
Evaluate side-chains
  96 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  196 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1082 THR
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   80 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 134 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0970
   chunk 77 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 136 optimal weight:    0.0670
   chunk 27 optimal weight:    4.9990
   chunk 144 optimal weight:    0.8980
   chunk 143 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 111 optimal weight:    8.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 GLN
A 342 GLN
** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5070 r_free = 0.5070 target = 0.266440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4837 r_free = 0.4837 target = 0.227909 restraints weight = 28882.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4886 r_free = 0.4886 target = 0.232894 restraints weight = 15455.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.236137 restraints weight = 9754.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.238317 restraints weight = 7024.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.239613 restraints weight = 5615.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.4903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1038
moved from start:          0.5321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14414  Z= 0.107
  Angle     :  0.543   9.174  20059  Z= 0.283
  Chirality :  0.038   0.223   2356
  Planarity :  0.004   0.046   2153
  Dihedral  : 19.499 177.265   3326
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.58 %
    Favored  : 87.67 %
  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: -1.20 (0.21), residues: 1447
  helix:  0.36 (0.19), residues: 682
  sheet: -0.75 (0.52), residues: 89
  loop : -2.07 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1122 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.011   0.001   PHE A 196 
 TRP   0.012   0.001   TRP A 476 
 HIS   0.009   0.001   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (14413)
  covalent geometry    : angle       0.54292 (20059)
  hydrogen bonds       : bond        0.03671 (  567)
  hydrogen bonds       : angle       4.66509 ( 1540)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.1757 (mmm) cc_final: 0.1099 (mmm)
REVERT: A  241 LEU cc_start: -0.2276 (OUTLIER) cc_final: -0.2959 (mp)
REVERT: A  346 LYS cc_start: 0.2033 (OUTLIER) cc_final: 0.1736 (pttm)
REVERT: A  694 MET cc_start: 0.0456 (ppp) cc_final: -0.1816 (mpp)
REVERT: A  904 GLU cc_start: 0.5433 (tt0) cc_final: 0.4183 (mt-10)
REVERT: A  970 PHE cc_start: 0.1913 (m-80) cc_final: 0.0600 (m-80)
REVERT: A  976 ARG cc_start: 0.1982 (ptp90) cc_final: -0.0166 (ptt-90)
REVERT: A 1060 ARG cc_start: 0.3300 (mtp85) cc_final: 0.2186 (mmm160)
REVERT: A 1089 MET cc_start: 0.0573 (tmm) cc_final: -0.0046 (tmm)
REVERT: C   30 LEU cc_start: -0.3357 (OUTLIER) cc_final: -0.3700 (tp)
REVERT: C   80 ILE cc_start: -0.3376 (OUTLIER) cc_final: -0.4567 (pt)
  outliers start: 21
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1407
  time to fit residues: 20.7798
Evaluate side-chains
  88 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  196 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   80 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 61 optimal weight:    0.0770
   chunk 34 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 137 optimal weight:    0.3980
   chunk 109 optimal weight:    4.9990
   chunk 135 optimal weight:    0.6980
   chunk 148 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 149 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A1091 GLN
A1264 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.266311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.227410 restraints weight = 28927.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.232444 restraints weight = 15493.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.235775 restraints weight = 9792.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4940 r_free = 0.4940 target = 0.237954 restraints weight = 7067.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.239098 restraints weight = 5663.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1123
moved from start:          0.5866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14414  Z= 0.099
  Angle     :  0.519   9.104  20059  Z= 0.269
  Chirality :  0.037   0.196   2356
  Planarity :  0.003   0.044   2153
  Dihedral  : 19.251 176.558   3326
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.08 %
    Favored  : 87.25 %
  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: -0.73 (0.22), residues: 1447
  helix:  0.80 (0.20), residues: 683
  sheet: -0.77 (0.48), residues: 99
  loop : -1.86 (0.22), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1122 
 TYR   0.012   0.001   TYR A 325 
 PHE   0.017   0.001   PHE A 704 
 TRP   0.013   0.001   TRP A 476 
 HIS   0.011   0.001   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 (14413)
  covalent geometry    : angle       0.51944 (20059)
  hydrogen bonds       : bond        0.03443 (  567)
  hydrogen bonds       : angle       4.31790 ( 1540)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.1340 (mmm) cc_final: 0.1009 (mmm)
REVERT: A  241 LEU cc_start: -0.2150 (OUTLIER) cc_final: -0.2912 (mp)
REVERT: A  694 MET cc_start: 0.0167 (ppp) cc_final: -0.1963 (mpp)
REVERT: A  904 GLU cc_start: 0.5647 (tt0) cc_final: 0.4335 (mt-10)
REVERT: A  970 PHE cc_start: 0.2125 (m-80) cc_final: 0.0888 (m-80)
REVERT: A  976 ARG cc_start: 0.2058 (ptp90) cc_final: -0.0118 (ptt-90)
REVERT: A 1060 ARG cc_start: 0.3656 (mtp85) cc_final: 0.2247 (tpt90)
REVERT: A 1089 MET cc_start: 0.0455 (tmm) cc_final: -0.0139 (tmm)
REVERT: C   30 LEU cc_start: -0.2745 (OUTLIER) cc_final: -0.3167 (tp)
REVERT: C   33 ARG cc_start: 0.5405 (mmt90) cc_final: 0.4982 (mmt180)
  outliers start: 20
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1236
  time to fit residues: 18.0104
Evaluate side-chains
  87 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  541 SER
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1082 THR
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 93 optimal weight:    0.0050
   chunk 79 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 89 optimal weight:    8.9990
   chunk 52 optimal weight:    0.6980
   chunk 146 optimal weight:    6.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    1.3198

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 985 HIS
A1264 HIS
A1286 ASN
C  61 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5078 r_free = 0.5078 target = 0.266255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.228789 restraints weight = 29688.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.233482 restraints weight = 16102.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.236586 restraints weight = 10279.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.4951 r_free = 0.4951 target = 0.238661 restraints weight = 7436.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4963 r_free = 0.4963 target = 0.239974 restraints weight = 5943.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.4889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1581
moved from start:          0.7572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  14414  Z= 0.161
  Angle     :  0.692  10.302  20059  Z= 0.355
  Chirality :  0.042   0.222   2356
  Planarity :  0.004   0.056   2153
  Dihedral  : 19.527 170.830   3326
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.00 %
    Favored  : 85.67 %
  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: -1.11 (0.21), residues: 1447
  helix:  0.24 (0.20), residues: 674
  sheet: -0.08 (0.55), residues: 77
  loop : -1.83 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 221 
 TYR   0.018   0.002   TYR A 515 
 PHE   0.047   0.002   PHE A 704 
 TRP   0.027   0.002   TRP A 476 
 HIS   0.022   0.002   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (14413)
  covalent geometry    : angle       0.69246 (20059)
  hydrogen bonds       : bond        0.04711 (  567)
  hydrogen bonds       : angle       4.94718 ( 1540)
  Misc. bond           : bond        0.00039 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A  241 LEU cc_start: -0.2069 (OUTLIER) cc_final: -0.2683 (mt)
REVERT: A  346 LYS cc_start: 0.2571 (OUTLIER) cc_final: 0.2100 (pttm)
REVERT: A  400 ARG cc_start: 0.4093 (tpt90) cc_final: 0.2994 (tpt90)
REVERT: A  694 MET cc_start: 0.0538 (ppp) cc_final: -0.2145 (mpp)
REVERT: A  904 GLU cc_start: 0.6360 (tt0) cc_final: 0.4893 (mt-10)
REVERT: A  939 MET cc_start: -0.2292 (ptt) cc_final: -0.3098 (ptp)
REVERT: A  970 PHE cc_start: 0.3038 (m-80) cc_final: 0.2531 (m-80)
REVERT: A  976 ARG cc_start: 0.2921 (ptp90) cc_final: 0.0117 (ptt-90)
REVERT: A 1060 ARG cc_start: 0.3259 (mtp85) cc_final: 0.2308 (mmm160)
REVERT: A 1089 MET cc_start: 0.0769 (tmm) cc_final: 0.0468 (tmm)
REVERT: A 1169 MET cc_start: 0.3491 (mtt) cc_final: 0.2654 (mtm)
REVERT: A 1264 HIS cc_start: 0.3505 (t-90) cc_final: 0.2817 (p90)
  outliers start: 28
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1270
  time to fit residues: 20.1825
Evaluate side-chains
  98 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  196 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  373 TYR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  642 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1082 THR
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1213 MET
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 137 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 122 optimal weight:    0.1980
   chunk 17 optimal weight:    0.5980
   chunk 138 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 139 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 142 optimal weight:    5.9990
   chunk 111 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
A 255 ASN
A 723 HIS
A 985 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5083 r_free = 0.5083 target = 0.266894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.228835 restraints weight = 29132.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.233719 restraints weight = 15863.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.236955 restraints weight = 10075.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.239145 restraints weight = 7256.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.240614 restraints weight = 5764.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.4891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1453
moved from start:          0.7824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14414  Z= 0.110
  Angle     :  0.567   9.762  20059  Z= 0.290
  Chirality :  0.038   0.224   2356
  Planarity :  0.003   0.045   2153
  Dihedral  : 19.229 173.991   3326
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.17 %
    Favored  : 84.67 %
  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: -0.78 (0.21), residues: 1447
  helix:  0.57 (0.20), residues: 683
  sheet: -0.15 (0.51), residues: 86
  loop : -1.75 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.014   0.001   TYR A 362 
 PHE   0.016   0.001   PHE A 256 
 TRP   0.017   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (14413)
  covalent geometry    : angle       0.56715 (20059)
  hydrogen bonds       : bond        0.03875 (  567)
  hydrogen bonds       : angle       4.43737 ( 1540)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   90 MET cc_start: -0.2077 (mmm) cc_final: -0.2353 (mmt)
REVERT: A  241 LEU cc_start: -0.2162 (OUTLIER) cc_final: -0.2931 (mt)
REVERT: A  346 LYS cc_start: 0.3014 (OUTLIER) cc_final: 0.2402 (pttm)
REVERT: A  407 ASN cc_start: -0.0055 (m-40) cc_final: -0.0333 (m-40)
REVERT: A  510 LYS cc_start: -0.1537 (ttmm) cc_final: -0.2189 (tmtt)
REVERT: A  694 MET cc_start: 0.0084 (ppp) cc_final: -0.2498 (mpp)
REVERT: A  904 GLU cc_start: 0.6258 (tt0) cc_final: 0.4733 (mt-10)
REVERT: A  939 MET cc_start: -0.1854 (ptt) cc_final: -0.2850 (ptp)
REVERT: A  970 PHE cc_start: 0.2731 (m-80) cc_final: 0.2420 (m-80)
REVERT: A  976 ARG cc_start: 0.3010 (ptp90) cc_final: -0.0013 (ptt-90)
REVERT: A  988 TYR cc_start: 0.1511 (t80) cc_final: 0.1261 (t80)
REVERT: A 1056 GLU cc_start: 0.1247 (mt-10) cc_final: 0.0749 (tm-30)
REVERT: A 1060 ARG cc_start: 0.3196 (mtp85) cc_final: 0.2208 (tpt90)
REVERT: A 1169 MET cc_start: 0.3103 (mtt) cc_final: 0.2146 (mtm)
REVERT: A 1333 ARG cc_start: 0.0463 (OUTLIER) cc_final: -0.1163 (ptm160)
REVERT: C   30 LEU cc_start: -0.2884 (OUTLIER) cc_final: -0.3417 (tp)
  outliers start: 26
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1412
  time to fit residues: 21.3341
Evaluate side-chains
  90 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  405 PHE
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 134 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 117 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 412 HIS
A 723 HIS
A1264 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5048 r_free = 0.5048 target = 0.262846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.227270 restraints weight = 31412.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.232035 restraints weight = 17575.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.235267 restraints weight = 11345.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.237442 restraints weight = 8256.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.238674 restraints weight = 6631.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.4873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1516
moved from start:          0.8425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  14414  Z= 0.124
  Angle     :  0.594   9.694  20059  Z= 0.303
  Chirality :  0.039   0.226   2356
  Planarity :  0.004   0.045   2153
  Dihedral  : 19.215 173.783   3326
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.50 %
    Favored  : 84.17 %
  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: -0.79 (0.22), residues: 1447
  helix:  0.59 (0.20), residues: 686
  sheet: -0.50 (0.50), residues: 94
  loop : -1.74 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 340 
 TYR   0.018   0.002   TYR A 359 
 PHE   0.018   0.002   PHE A 491 
 TRP   0.021   0.001   TRP A 476 
 HIS   0.017   0.002   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (14413)
  covalent geometry    : angle       0.59419 (20059)
  hydrogen bonds       : bond        0.04178 (  567)
  hydrogen bonds       : angle       4.49598 ( 1540)
  Misc. bond           : bond        0.00035 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 LEU cc_start: -0.2280 (OUTLIER) cc_final: -0.3060 (mt)
REVERT: A  346 LYS cc_start: 0.3171 (OUTLIER) cc_final: 0.2626 (pttm)
REVERT: A  510 LYS cc_start: -0.1848 (ttmm) cc_final: -0.2324 (tmtt)
REVERT: A  631 MET cc_start: -0.1504 (mmm) cc_final: -0.2314 (mmm)
REVERT: A  904 GLU cc_start: 0.5941 (tt0) cc_final: 0.4610 (mt-10)
REVERT: A  939 MET cc_start: -0.1371 (ptt) cc_final: -0.2296 (ptp)
REVERT: A  970 PHE cc_start: 0.2879 (m-80) cc_final: 0.2537 (m-80)
REVERT: A  976 ARG cc_start: 0.2987 (ptp90) cc_final: -0.0074 (ptt-90)
REVERT: A  988 TYR cc_start: 0.1266 (t80) cc_final: 0.0999 (t80)
REVERT: A 1056 GLU cc_start: 0.1697 (mt-10) cc_final: 0.1059 (tm-30)
REVERT: A 1060 ARG cc_start: 0.2596 (mtp85) cc_final: 0.2031 (tpt90)
REVERT: A 1169 MET cc_start: 0.3241 (mtt) cc_final: 0.2227 (mtm)
REVERT: A 1333 ARG cc_start: 0.1096 (OUTLIER) cc_final: -0.0643 (ptm160)
REVERT: C    1 MET cc_start: 0.2508 (ptt) cc_final: -0.0485 (mmt)
REVERT: C   30 LEU cc_start: -0.3154 (OUTLIER) cc_final: -0.3605 (tp)
  outliers start: 28
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1301
  time to fit residues: 19.7177
Evaluate side-chains
  95 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  405 PHE
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  891 LEU
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1082 THR
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 142 optimal weight:    0.7980
   chunk 146 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 119 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 412 HIS
A 612 ASN
A 863 ASN
A1264 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5055 r_free = 0.5055 target = 0.263135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.227763 restraints weight = 31509.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.232514 restraints weight = 17500.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.235684 restraints weight = 11303.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.237856 restraints weight = 8228.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.239136 restraints weight = 6590.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1513
moved from start:          0.8724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  14414  Z= 0.114
  Angle     :  0.577   9.176  20059  Z= 0.295
  Chirality :  0.038   0.214   2356
  Planarity :  0.003   0.045   2153
  Dihedral  : 19.144 173.603   3326
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.17 %
    Favored  : 84.67 %
  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: -0.70 (0.22), residues: 1447
  helix:  0.68 (0.20), residues: 685
  sheet: -0.53 (0.51), residues: 94
  loop : -1.70 (0.23), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.016   0.001   TYR A 359 
 PHE   0.017   0.002   PHE A 119 
 TRP   0.018   0.001   TRP A 476 
 HIS   0.011   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (14413)
  covalent geometry    : angle       0.57737 (20059)
  hydrogen bonds       : bond        0.04228 (  567)
  hydrogen bonds       : angle       4.41849 ( 1540)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  241 LEU cc_start: -0.2396 (OUTLIER) cc_final: -0.3126 (mt)
REVERT: A  346 LYS cc_start: 0.3640 (OUTLIER) cc_final: 0.3103 (pttm)
REVERT: A  510 LYS cc_start: -0.1764 (ttmm) cc_final: -0.2234 (tmtt)
REVERT: A  631 MET cc_start: -0.1664 (mmm) cc_final: -0.2378 (mmm)
REVERT: A  904 GLU cc_start: 0.5885 (tt0) cc_final: 0.4578 (mt-10)
REVERT: A  939 MET cc_start: -0.1377 (ptt) cc_final: -0.2336 (ptp)
REVERT: A  970 PHE cc_start: 0.3052 (m-80) cc_final: 0.2677 (m-80)
REVERT: A  976 ARG cc_start: 0.2819 (ptp90) cc_final: -0.0223 (ptt-90)
REVERT: A  988 TYR cc_start: 0.1028 (t80) cc_final: 0.0816 (t80)
REVERT: A 1056 GLU cc_start: 0.1636 (mt-10) cc_final: 0.1075 (tm-30)
REVERT: A 1060 ARG cc_start: 0.2568 (mtp85) cc_final: 0.1862 (tpt90)
REVERT: A 1169 MET cc_start: 0.3075 (mtt) cc_final: 0.2062 (mtm)
REVERT: A 1333 ARG cc_start: 0.0849 (OUTLIER) cc_final: -0.0710 (ptm160)
REVERT: C    1 MET cc_start: 0.2285 (ptt) cc_final: -0.0528 (mmt)
REVERT: C   30 LEU cc_start: -0.3248 (OUTLIER) cc_final: -0.3609 (tp)
  outliers start: 26
  outliers final: 17
  residues processed: 102
  average time/residue: 0.1379
  time to fit residues: 20.3682
Evaluate side-chains
  97 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  405 PHE
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1082 THR
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1264 HIS
Chi-restraints excluded: chain A residue 1326 TYR
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 90 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 116 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 148 optimal weight:    0.7980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
A 342 GLN
A 412 HIS
A1264 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.265465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.227373 restraints weight = 29604.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.231855 restraints weight = 16732.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4919 r_free = 0.4919 target = 0.234895 restraints weight = 10910.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.236723 restraints weight = 7998.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 69)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.238286 restraints weight = 6514.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.4880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1525
moved from start:          0.9035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.066  14414  Z= 0.117
  Angle     :  0.582   8.978  20059  Z= 0.297
  Chirality :  0.038   0.202   2356
  Planarity :  0.003   0.045   2153
  Dihedral  : 19.092 174.165   3326
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.58 %
    Favored  : 84.50 %
  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: -0.69 (0.22), residues: 1447
  helix:  0.72 (0.20), residues: 684
  sheet: -0.48 (0.52), residues: 94
  loop : -1.74 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 400 
 TYR   0.016   0.001   TYR A 359 
 PHE   0.015   0.002   PHE A 119 
 TRP   0.018   0.001   TRP A 476 
 HIS   0.025   0.002   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (14413)
  covalent geometry    : angle       0.58166 (20059)
  hydrogen bonds       : bond        0.04182 (  567)
  hydrogen bonds       : angle       4.36072 ( 1540)
  Misc. bond           : bond        0.00033 (    1)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A  241 LEU cc_start: -0.2358 (OUTLIER) cc_final: -0.3167 (mt)
REVERT: A  346 LYS cc_start: 0.3768 (OUTLIER) cc_final: 0.3172 (pttm)
REVERT: A  400 ARG cc_start: 0.4073 (OUTLIER) cc_final: 0.1621 (tpt170)
REVERT: A  510 LYS cc_start: -0.1784 (ttmm) cc_final: -0.2235 (tmtt)
REVERT: A  631 MET cc_start: -0.1700 (mmm) cc_final: -0.2395 (mmm)
REVERT: A  694 MET cc_start: 0.1631 (tmm) cc_final: 0.1398 (tmm)
REVERT: A  904 GLU cc_start: 0.5875 (tt0) cc_final: 0.4575 (mt-10)
REVERT: A  939 MET cc_start: -0.1166 (ptt) cc_final: -0.2113 (ptp)
REVERT: A  970 PHE cc_start: 0.3109 (m-80) cc_final: 0.2720 (m-80)
REVERT: A  976 ARG cc_start: 0.2734 (ptp90) cc_final: -0.0174 (ptt-90)
REVERT: A  988 TYR cc_start: 0.0920 (t80) cc_final: 0.0715 (t80)
REVERT: A 1056 GLU cc_start: 0.1749 (mt-10) cc_final: 0.1224 (tp30)
REVERT: A 1060 ARG cc_start: 0.2602 (mtp85) cc_final: 0.1877 (tpt90)
REVERT: A 1169 MET cc_start: 0.2971 (mtt) cc_final: 0.1987 (mtm)
REVERT: A 1264 HIS cc_start: 0.3029 (OUTLIER) cc_final: 0.2752 (t-170)
REVERT: A 1333 ARG cc_start: 0.1077 (OUTLIER) cc_final: -0.0547 (ptm160)
REVERT: C   30 LEU cc_start: -0.3495 (OUTLIER) cc_final: -0.3827 (tp)
REVERT: C   37 ASP cc_start: 0.7010 (t70) cc_final: 0.6248 (m-30)
REVERT: C   71 GLU cc_start: -0.1604 (OUTLIER) cc_final: -0.2440 (pm20)
  outliers start: 23
  outliers final: 15
  residues processed: 98
  average time/residue: 0.1441
  time to fit residues: 20.5107
Evaluate side-chains
  100 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  400 ARG
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  405 PHE
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1082 THR
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1264 HIS
Chi-restraints excluded: chain A residue 1326 TYR
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 154 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 151 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5050 r_free = 0.5050 target = 0.255660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.222538 restraints weight = 31194.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.225514 restraints weight = 19903.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.228709 restraints weight = 13372.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4833 r_free = 0.4833 target = 0.230080 restraints weight = 8960.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4837 r_free = 0.4837 target = 0.230467 restraints weight = 8649.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1898
moved from start:          1.0099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14414  Z= 0.179
  Angle     :  0.749  10.012  20059  Z= 0.387
  Chirality :  0.043   0.217   2356
  Planarity :  0.005   0.049   2153
  Dihedral  : 19.502 170.566   3326
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.58 %
    Favored  : 84.17 %
  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: -1.33 (0.21), residues: 1447
  helix:  0.06 (0.20), residues: 683
  sheet: -1.15 (0.50), residues: 103
  loop : -1.85 (0.22), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 340 
 TYR   0.024   0.002   TYR A 515 
 PHE   0.026   0.003   PHE A 256 
 TRP   0.032   0.002   TRP A 476 
 HIS   0.041   0.003   HIS A1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (14413)
  covalent geometry    : angle       0.74860 (20059)
  hydrogen bonds       : bond        0.05309 (  567)
  hydrogen bonds       : angle       5.05422 ( 1540)
  Misc. bond           : bond        0.00070 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2649.56 seconds
wall clock time: 46 minutes 27.28 seconds (2787.28 seconds total)