Starting phenix.real_space_refine
on Thu Jun 12 21:55:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5vzl_8749/06_2025/5vzl_8749_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5vzl_8749/06_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_8749/06_2025/5vzl_8749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5vzl_8749/06_2025/5vzl_8749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5vzl_8749/06_2025/5vzl_8749_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5vzl_8749/06_2025/5vzl_8749_neut.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 10}
          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: 8.66, per 1000 atoms: 0.62
  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: 3.44
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 4.99
  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: 6.46

  Time building geometry restraints manager: 4.11 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:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.020
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.610
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.011   0.003   TRP A 464 
 HIS   0.007   0.002   HIS A1241 
 PHE   0.020   0.003   PHE A1008 
 TYR   0.028   0.003   TYR A 973 
 ARG   0.015   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15738 (  567)
  hydrogen bonds       : angle       9.97298 ( 1540)
  covalent geometry    : bond        0.00573 (14413)
  covalent geometry    : angle       0.95819 (20059)
  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  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ARG cc_start: -0.3469 (OUTLIER) cc_final: -0.3722 (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: 0.4064 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 124
  average time/residue: 0.3144
  time to fit residues: 54.7537
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  : 1.249 
-------------------------------------------------------------------------------
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 130 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 121 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   chunk 140 optimal weight:    0.0370
   overall best weight:    1.1062

-------------------------------------------------------------------------------
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 224 ASN
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5043 r_free = 0.5043 target = 0.265186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.228254 restraints weight = 30553.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.233455 restraints weight = 16376.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.236794 restraints weight = 10316.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.4787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0768
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14414  Z= 0.154
  Angle     :  0.663   9.534  20059  Z= 0.344
  Chirality :  0.040   0.254   2356
  Planarity :  0.005   0.066   2153
  Dihedral  : 19.981 179.832   3330
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  6.33 %
    Favored  : 92.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.20), residues: 1447
  helix: -0.96 (0.18), residues: 688
  sheet: -1.78 (0.42), residues: 120
  loop : -2.21 (0.23), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 476 
 HIS   0.011   0.002   HIS A 328 
 PHE   0.015   0.002   PHE A 164 
 TYR   0.020   0.002   TYR A 155 
 ARG   0.008   0.001   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  567)
  hydrogen bonds       : angle       5.50919 ( 1540)
  covalent geometry    : bond        0.00321 (14413)
  covalent geometry    : angle       0.66327 (20059)
  Misc. bond           : bond        0.00034 (    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
  112 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.1861 (mmm) cc_final: 0.1522 (mmm)
REVERT: A  194 GLN cc_start: -0.2404 (OUTLIER) cc_final: -0.3450 (mm-40)
REVERT: A  207 ASP cc_start: 0.5519 (t0) cc_final: 0.5147 (p0)
REVERT: A  241 LEU cc_start: -0.1565 (OUTLIER) cc_final: -0.2376 (mp)
REVERT: A  822 MET cc_start: -0.3258 (mmm) cc_final: -0.4058 (mtt)
REVERT: A  904 GLU cc_start: 0.4578 (tt0) cc_final: 0.3450 (mt-10)
REVERT: A 1060 ARG cc_start: 0.3337 (mtp85) cc_final: 0.2331 (mmm160)
REVERT: A 1095 VAL cc_start: -0.1027 (t) cc_final: -0.1451 (p)
REVERT: A 1328 ASP cc_start: 0.2658 (p0) cc_final: 0.2089 (t70)
  outliers start: 17
  outliers final: 5
  residues processed: 110
  average time/residue: 0.3114
  time to fit residues: 50.9461
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  : 1.706 
-------------------------------------------------------------------------------
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 1015 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1082 THR
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 145 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 142 optimal weight:    0.0670
   chunk 126 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0040
   chunk 152 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 122 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8136

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 817 GLN
A1091 GLN
A1264 HIS
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  25 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5064 r_free = 0.5064 target = 0.266465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.226416 restraints weight = 29016.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.231449 restraints weight = 15475.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.234761 restraints weight = 9782.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.4816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0961
moved from start:          0.4244

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= 0.124
  Angle     :  0.575   9.425  20059  Z= 0.298
  Chirality :  0.038   0.238   2356
  Planarity :  0.004   0.048   2153
  Dihedral  : 19.637 179.223   3326
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  8.00 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.21), residues: 1447
  helix: -0.02 (0.19), residues: 700
  sheet: -1.05 (0.51), residues: 91
  loop : -2.08 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 328 
 PHE   0.011   0.001   PHE C  73 
 TYR   0.013   0.001   TYR A 656 
 ARG   0.010   0.001   ARG A 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03999 (  567)
  hydrogen bonds       : angle       4.88979 ( 1540)
  covalent geometry    : bond        0.00253 (14413)
  covalent geometry    : angle       0.57486 (20059)
  Misc. bond           : bond        0.00026 (    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
  110 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.3704 (OUTLIER) cc_final: 0.3492 (m-10)
REVERT: A  119 PHE cc_start: -0.0836 (m-10) cc_final: -0.1346 (m-10)
REVERT: A  161 MET cc_start: 0.1952 (mmm) cc_final: 0.1522 (mmm)
REVERT: A  241 LEU cc_start: -0.2005 (OUTLIER) cc_final: -0.2704 (mp)
REVERT: A  684 LYS cc_start: 0.7137 (mtmt) cc_final: 0.6899 (mtmm)
REVERT: A  694 MET cc_start: -0.0725 (ppp) cc_final: -0.2376 (mpp)
REVERT: A  904 GLU cc_start: 0.5182 (tt0) cc_final: 0.3955 (mt-10)
REVERT: A  970 PHE cc_start: 0.2056 (m-80) cc_final: 0.0745 (m-80)
REVERT: A  976 ARG cc_start: 0.2671 (ptp-170) cc_final: 0.0106 (ptt180)
REVERT: A 1060 ARG cc_start: 0.3245 (mtp85) cc_final: 0.2279 (mmm160)
REVERT: A 1089 MET cc_start: 0.0650 (tmm) cc_final: 0.0041 (tmm)
REVERT: C   30 LEU cc_start: -0.2205 (OUTLIER) cc_final: -0.2686 (tp)
REVERT: C   80 ILE cc_start: -0.2568 (OUTLIER) cc_final: -0.3893 (pt)
  outliers start: 21
  outliers final: 9
  residues processed: 107
  average time/residue: 0.2855
  time to fit residues: 45.0545
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  : 1.240 
-------------------------------------------------------------------------------
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  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 1338 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0070
   chunk 148 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 59 optimal weight:    8.9990
   chunk 135 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    2.7804

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 920 GLN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1286 ASN
A1295 ASN
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5034 r_free = 0.5034 target = 0.261327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.227906 restraints weight = 32261.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.232345 restraints weight = 17681.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.235289 restraints weight = 11387.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.4832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1797
moved from start:          0.8118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  14414  Z= 0.273
  Angle     :  1.042  12.056  20059  Z= 0.537
  Chirality :  0.054   0.350   2356
  Planarity :  0.008   0.128   2153
  Dihedral  : 20.577 168.823   3326
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.02 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 10.17 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.19), residues: 1447
  helix: -1.11 (0.18), residues: 663
  sheet: -1.48 (0.49), residues: 89
  loop : -2.44 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A 476 
 HIS   0.016   0.003   HIS A 167 
 PHE   0.033   0.004   PHE A1181 
 TYR   0.037   0.004   TYR A 515 
 ARG   0.013   0.002   ARG A1122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07213 (  567)
  hydrogen bonds       : angle       6.58937 ( 1540)
  covalent geometry    : bond        0.00579 (14413)
  covalent geometry    : angle       1.04216 (20059)
  Misc. bond           : bond        0.00082 (    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
  137 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 94
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.1895 (mmm) cc_final: 0.1524 (mmm)
REVERT: A  223 GLU cc_start: -0.2317 (OUTLIER) cc_final: -0.3446 (pt0)
REVERT: A  694 MET cc_start: 0.0049 (ppp) cc_final: -0.2594 (mpp)
REVERT: A  703 THR cc_start: 0.2367 (OUTLIER) cc_final: 0.2017 (t)
REVERT: A  822 MET cc_start: -0.4275 (mtt) cc_final: -0.4501 (mtp)
REVERT: A  904 GLU cc_start: 0.5451 (tt0) cc_final: 0.4221 (mt-10)
REVERT: A  970 PHE cc_start: 0.3718 (m-80) cc_final: 0.2841 (m-80)
REVERT: A  976 ARG cc_start: 0.3175 (ptp-170) cc_final: -0.0356 (ptt-90)
REVERT: A 1060 ARG cc_start: 0.3424 (mtp85) cc_final: 0.2476 (mmm160)
REVERT: A 1089 MET cc_start: 0.1365 (tmm) cc_final: 0.0896 (tmm)
REVERT: A 1264 HIS cc_start: 0.4121 (t-170) cc_final: 0.3415 (p-80)
REVERT: A 1333 ARG cc_start: 0.1281 (OUTLIER) cc_final: -0.0003 (ptm160)
REVERT: C    1 MET cc_start: 0.2347 (ptt) cc_final: -0.0498 (mmt)
REVERT: C   33 ARG cc_start: 0.4808 (mmt90) cc_final: 0.4462 (mmt180)
REVERT: C   34 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4546 (m)
REVERT: C   37 ASP cc_start: 0.6877 (t70) cc_final: 0.6445 (m-30)
  outliers start: 43
  outliers final: 16
  residues processed: 130
  average time/residue: 0.2825
  time to fit residues: 53.7159
Evaluate side-chains
  102 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  196 PHE
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  338 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 1328 ASP
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   79 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 145 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 148 optimal weight:    0.4980
   chunk 127 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 108 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 HIS
A 723 HIS
** A 985 HIS ** 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 = 0.5045 r_free = 0.5045 target = 0.263052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.227807 restraints weight = 32030.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.232512 restraints weight = 18017.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.235721 restraints weight = 11555.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1682
moved from start:          0.8378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14414  Z= 0.148
  Angle     :  0.675   9.833  20059  Z= 0.350
  Chirality :  0.043   0.240   2356
  Planarity :  0.004   0.061   2153
  Dihedral  : 20.044 170.561   3326
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.08 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.20), residues: 1447
  helix: -0.58 (0.19), residues: 687
  sheet: -1.31 (0.46), residues: 99
  loop : -2.26 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 476 
 HIS   0.007   0.001   HIS A 167 
 PHE   0.020   0.002   PHE A 491 
 TYR   0.017   0.002   TYR A 515 
 ARG   0.007   0.001   ARG A1122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04852 (  567)
  hydrogen bonds       : angle       5.33653 ( 1540)
  covalent geometry    : bond        0.00300 (14413)
  covalent geometry    : angle       0.67494 (20059)
  Misc. bond           : bond        0.00067 (    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
  127 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 92
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.1519 (mmm) cc_final: 0.1207 (mmm)
REVERT: A  194 GLN cc_start: -0.1044 (OUTLIER) cc_final: -0.2253 (mm-40)
REVERT: A  346 LYS cc_start: 0.3285 (OUTLIER) cc_final: 0.2344 (pttm)
REVERT: A  401 LYS cc_start: 0.3849 (mmtt) cc_final: 0.3627 (mmmt)
REVERT: A  510 LYS cc_start: -0.0806 (tttt) cc_final: -0.1541 (tmtt)
REVERT: A  694 MET cc_start: 0.0656 (ppp) cc_final: -0.2286 (mpp)
REVERT: A  822 MET cc_start: -0.4195 (mtt) cc_final: -0.4643 (mtp)
REVERT: A  904 GLU cc_start: 0.5774 (tt0) cc_final: 0.4593 (mt-10)
REVERT: A  939 MET cc_start: -0.1212 (ptt) cc_final: -0.2123 (ptp)
REVERT: A  970 PHE cc_start: 0.3304 (m-80) cc_final: 0.2814 (m-80)
REVERT: A  976 ARG cc_start: 0.3377 (ptp-170) cc_final: -0.0069 (ptt-90)
REVERT: A 1056 GLU cc_start: 0.1314 (mt-10) cc_final: 0.0638 (tm-30)
REVERT: A 1060 ARG cc_start: 0.3381 (mtp85) cc_final: 0.2441 (mmm160)
REVERT: A 1264 HIS cc_start: 0.3546 (t-90) cc_final: 0.1945 (p90)
REVERT: A 1268 GLU cc_start: 0.2131 (mt-10) cc_final: 0.1199 (mm-30)
REVERT: A 1333 ARG cc_start: 0.0067 (OUTLIER) cc_final: -0.1282 (ptm160)
REVERT: C   33 ARG cc_start: 0.4905 (mmt90) cc_final: 0.4247 (mmt90)
REVERT: C   37 ASP cc_start: 0.6988 (t70) cc_final: 0.6619 (m-30)
REVERT: C   77 MET cc_start: 0.0800 (mmp) cc_final: -0.0152 (ptt)
  outliers start: 35
  outliers final: 16
  residues processed: 122
  average time/residue: 0.3273
  time to fit residues: 61.3780
Evaluate side-chains
  102 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  398 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 1168 ILE
Chi-restraints excluded: chain A residue 1213 MET
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 86 optimal weight:    0.0050
   chunk 126 optimal weight:    0.1980
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 ASN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 342 GLN
A 723 HIS
A 863 ASN
A1241 HIS
A1295 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5059 r_free = 0.5059 target = 0.264157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.229292 restraints weight = 32108.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4886 r_free = 0.4886 target = 0.233883 restraints weight = 18064.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.237054 restraints weight = 11662.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.4851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1576
moved from start:          0.8594

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= 0.114
  Angle     :  0.599   9.583  20059  Z= 0.308
  Chirality :  0.040   0.246   2356
  Planarity :  0.004   0.047   2153
  Dihedral  : 19.700 175.176   3326
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.92 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.21), residues: 1447
  helix: -0.07 (0.20), residues: 690
  sheet: -0.65 (0.51), residues: 88
  loop : -2.06 (0.21), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.011   0.001   PHE A1008 
 TYR   0.020   0.002   TYR A 325 
 ARG   0.006   0.000   ARG A1122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04264 (  567)
  hydrogen bonds       : angle       4.80654 ( 1540)
  covalent geometry    : bond        0.00227 (14413)
  covalent geometry    : angle       0.59881 (20059)
  Misc. bond           : bond        0.00043 (    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
  119 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 1.759 
Fit side-chains
REVERT: A  132 TYR cc_start: 0.0675 (OUTLIER) cc_final: -0.0643 (m-80)
REVERT: A  161 MET cc_start: 0.1555 (mmm) cc_final: 0.1165 (mmm)
REVERT: A  252 PHE cc_start: 0.0848 (OUTLIER) cc_final: -0.0231 (m-80)
REVERT: A  346 LYS cc_start: 0.3467 (OUTLIER) cc_final: 0.2410 (pttm)
REVERT: A  354 GLN cc_start: -0.1280 (OUTLIER) cc_final: -0.2175 (mt0)
REVERT: A  510 LYS cc_start: -0.1196 (tttt) cc_final: -0.1813 (tmtt)
REVERT: A  631 MET cc_start: -0.0828 (mmm) cc_final: -0.1663 (mmm)
REVERT: A  694 MET cc_start: 0.0206 (ppp) cc_final: -0.2633 (mpp)
REVERT: A  904 GLU cc_start: 0.5786 (tt0) cc_final: 0.4604 (mt-10)
REVERT: A  970 PHE cc_start: 0.3253 (m-80) cc_final: 0.2787 (m-80)
REVERT: A  976 ARG cc_start: 0.3395 (ptp-170) cc_final: -0.0189 (ptt-90)
REVERT: A 1056 GLU cc_start: 0.1518 (mt-10) cc_final: 0.0851 (tm-30)
REVERT: A 1060 ARG cc_start: 0.2883 (mtp85) cc_final: 0.2031 (tpt90)
REVERT: A 1264 HIS cc_start: 0.3228 (t-90) cc_final: 0.2672 (p90)
REVERT: C   33 ARG cc_start: 0.5100 (mmt90) cc_final: 0.4833 (mmt180)
REVERT: C   37 ASP cc_start: 0.6806 (t70) cc_final: 0.6391 (m-30)
REVERT: C   77 MET cc_start: 0.0667 (mmp) cc_final: 0.0078 (ptm)
REVERT: C   79 THR cc_start: 0.1276 (p) cc_final: -0.0707 (m)
  outliers start: 25
  outliers final: 12
  residues processed: 117
  average time/residue: 0.4623
  time to fit residues: 81.1908
Evaluate side-chains
  106 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 2.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  587 PHE
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1213 MET
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 38 optimal weight:    0.2980
   chunk 99 optimal weight:    1.9990
   chunk 129 optimal weight:    0.8980
   chunk 130 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5055 r_free = 0.5055 target = 0.263624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.228812 restraints weight = 31759.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.233440 restraints weight = 17854.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.236646 restraints weight = 11589.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.4844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1619
moved from start:          0.9021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  14414  Z= 0.120
  Angle     :  0.614  10.685  20059  Z= 0.310
  Chirality :  0.040   0.242   2356
  Planarity :  0.004   0.046   2153
  Dihedral  : 19.521 174.955   3326
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.21), residues: 1447
  helix:  0.14 (0.20), residues: 692
  sheet: -0.73 (0.52), residues: 88
  loop : -1.98 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 476 
 HIS   0.012   0.001   HIS A1241 
 PHE   0.014   0.001   PHE A 491 
 TYR   0.024   0.002   TYR A 656 
 ARG   0.003   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04204 (  567)
  hydrogen bonds       : angle       4.71037 ( 1540)
  covalent geometry    : bond        0.00239 (14413)
  covalent geometry    : angle       0.61377 (20059)
  Misc. bond           : bond        0.00042 (    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
  121 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.1088 (OUTLIER) cc_final: -0.0564 (m-80)
REVERT: A  161 MET cc_start: 0.1740 (mmm) cc_final: 0.1293 (mmm)
REVERT: A  194 GLN cc_start: -0.1170 (OUTLIER) cc_final: -0.2614 (mm-40)
REVERT: A  252 PHE cc_start: 0.0647 (OUTLIER) cc_final: -0.0282 (m-80)
REVERT: A  346 LYS cc_start: 0.3759 (OUTLIER) cc_final: 0.2709 (pttm)
REVERT: A  354 GLN cc_start: -0.1258 (OUTLIER) cc_final: -0.1881 (tt0)
REVERT: A  510 LYS cc_start: -0.0775 (tttt) cc_final: -0.1553 (tmtt)
REVERT: A  631 MET cc_start: -0.0638 (mmm) cc_final: -0.1380 (mmm)
REVERT: A  904 GLU cc_start: 0.5736 (tt0) cc_final: 0.4687 (mt-10)
REVERT: A  939 MET cc_start: -0.1328 (ptt) cc_final: -0.2271 (ptp)
REVERT: A  970 PHE cc_start: 0.3084 (m-80) cc_final: 0.2699 (m-80)
REVERT: A  976 ARG cc_start: 0.3014 (ptp-170) cc_final: -0.0174 (ptt-90)
REVERT: A 1056 GLU cc_start: 0.1782 (mt-10) cc_final: 0.1133 (tp30)
REVERT: A 1060 ARG cc_start: 0.2763 (mtp85) cc_final: 0.1983 (tpt90)
REVERT: A 1264 HIS cc_start: 0.3210 (t-90) cc_final: 0.2650 (p-80)
REVERT: A 1333 ARG cc_start: -0.0033 (OUTLIER) cc_final: -0.1541 (ptm160)
REVERT: C   37 ASP cc_start: 0.6827 (t70) cc_final: 0.6358 (m-30)
REVERT: C   54 LYS cc_start: -0.2423 (OUTLIER) cc_final: -0.3212 (tppt)
REVERT: C   77 MET cc_start: 0.0873 (mmp) cc_final: 0.0178 (ppp)
  outliers start: 32
  outliers final: 18
  residues processed: 114
  average time/residue: 0.2861
  time to fit residues: 48.2482
Evaluate side-chains
  112 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  405 PHE
Chi-restraints excluded: chain A residue  430 TYR
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 1159 SER
Chi-restraints excluded: chain A residue 1213 MET
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1333 ARG
Chi-restraints excluded: chain A residue 1338 SER
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   54 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0270
   chunk 116 optimal weight:   10.0000
   chunk 150 optimal weight:    0.0020
   chunk 82 optimal weight:    0.0270
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 98 optimal weight:    0.0010
   chunk 16 optimal weight:    0.0980
   chunk 121 optimal weight:    0.0570
   overall best weight:    0.0228

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5066 r_free = 0.5066 target = 0.265290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.229986 restraints weight = 31114.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.234884 restraints weight = 17268.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.237977 restraints weight = 11011.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.4847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1375
moved from start:          0.8924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14414  Z= 0.101
  Angle     :  0.567  11.882  20059  Z= 0.283
  Chirality :  0.038   0.223   2356
  Planarity :  0.003   0.042   2153
  Dihedral  : 19.206 177.540   3326
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.42 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.22), residues: 1447
  helix:  0.58 (0.20), residues: 694
  sheet: -0.43 (0.49), residues: 106
  loop : -1.86 (0.22), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  18 
 HIS   0.014   0.001   HIS A1241 
 PHE   0.021   0.001   PHE A1327 
 TYR   0.024   0.001   TYR A1237 
 ARG   0.006   0.000   ARG A 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  567)
  hydrogen bonds       : angle       4.24355 ( 1540)
  covalent geometry    : bond        0.00199 (14413)
  covalent geometry    : angle       0.56675 (20059)
  Misc. bond           : bond        0.00017 (    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
  101 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.1380 (mmm) cc_final: 0.1120 (mmm)
REVERT: A  194 GLN cc_start: -0.1914 (OUTLIER) cc_final: -0.3015 (mm-40)
REVERT: A  346 LYS cc_start: 0.3604 (OUTLIER) cc_final: 0.2704 (pttm)
REVERT: A  510 LYS cc_start: -0.0925 (tttt) cc_final: -0.1560 (tmtt)
REVERT: A  631 MET cc_start: -0.1599 (mmm) cc_final: -0.2102 (mmm)
REVERT: A  939 MET cc_start: -0.1208 (ptt) cc_final: -0.2319 (ptp)
REVERT: A  970 PHE cc_start: 0.2641 (m-80) cc_final: 0.1937 (m-80)
REVERT: A  976 ARG cc_start: 0.2624 (ptp-170) cc_final: -0.0280 (ptt-90)
REVERT: A 1056 GLU cc_start: 0.1765 (mt-10) cc_final: 0.1272 (tp30)
REVERT: A 1060 ARG cc_start: 0.2289 (mtp85) cc_final: 0.1569 (tpt90)
REVERT: A 1264 HIS cc_start: 0.3262 (t-90) cc_final: 0.2677 (p-80)
REVERT: C   33 ARG cc_start: 0.6385 (mmt180) cc_final: 0.6174 (mmt180)
REVERT: C   37 ASP cc_start: 0.6914 (t70) cc_final: 0.6238 (m-30)
REVERT: C   77 MET cc_start: 0.1132 (mmp) cc_final: 0.0470 (ptt)
  outliers start: 12
  outliers final: 10
  residues processed: 98
  average time/residue: 0.2974
  time to fit residues: 42.9990
Evaluate side-chains
  93 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  587 PHE
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1326 TYR
Chi-restraints excluded: chain A residue 1352 ILE
Chi-restraints excluded: chain C residue   28 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 147 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 145 optimal weight:    0.5980
   chunk 63 optimal weight:    8.9990
   chunk 113 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5057 r_free = 0.5057 target = 0.263593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.229137 restraints weight = 32190.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.233872 restraints weight = 18263.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.237147 restraints weight = 11883.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1839
moved from start:          0.9740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14414  Z= 0.149
  Angle     :  0.664  10.907  20059  Z= 0.336
  Chirality :  0.041   0.219   2356
  Planarity :  0.004   0.046   2153
  Dihedral  : 19.368 172.191   3326
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.58 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.21), residues: 1447
  helix:  0.21 (0.20), residues: 699
  sheet: -1.26 (0.47), residues: 105
  loop : -1.81 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 476 
 HIS   0.010   0.002   HIS A1241 
 PHE   0.021   0.002   PHE A 491 
 TYR   0.028   0.002   TYR A 656 
 ARG   0.009   0.001   ARG A1122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  567)
  hydrogen bonds       : angle       4.73442 ( 1540)
  covalent geometry    : bond        0.00305 (14413)
  covalent geometry    : angle       0.66360 (20059)
  Misc. bond           : bond        0.00049 (    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
  113 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 1.532 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.1690 (OUTLIER) cc_final: 0.0026 (m-80)
REVERT: A  161 MET cc_start: 0.1252 (mmm) cc_final: 0.0992 (mmm)
REVERT: A  194 GLN cc_start: -0.1187 (OUTLIER) cc_final: -0.2752 (mm-40)
REVERT: A  252 PHE cc_start: 0.0975 (OUTLIER) cc_final: -0.0001 (m-80)
REVERT: A  346 LYS cc_start: 0.4424 (OUTLIER) cc_final: 0.3428 (pttm)
REVERT: A  379 ILE cc_start: 0.6132 (mm) cc_final: 0.5478 (mt)
REVERT: A  631 MET cc_start: -0.1522 (mmm) cc_final: -0.1956 (mmm)
REVERT: A  904 GLU cc_start: 0.5941 (tt0) cc_final: 0.4830 (mt-10)
REVERT: A  970 PHE cc_start: 0.3292 (m-80) cc_final: 0.2683 (m-80)
REVERT: A  976 ARG cc_start: 0.3367 (ptp-170) cc_final: 0.0333 (ptt-90)
REVERT: A 1056 GLU cc_start: 0.1943 (mt-10) cc_final: 0.1446 (tp30)
REVERT: A 1060 ARG cc_start: 0.2893 (mtp85) cc_final: 0.2182 (tpt90)
REVERT: C   30 LEU cc_start: -0.2401 (OUTLIER) cc_final: -0.3055 (tp)
REVERT: C   31 ILE cc_start: 0.5052 (OUTLIER) cc_final: 0.4689 (pp)
REVERT: C   37 ASP cc_start: 0.6873 (t70) cc_final: 0.6139 (m-30)
REVERT: C   54 LYS cc_start: -0.1470 (OUTLIER) cc_final: -0.2440 (tmtt)
REVERT: C   77 MET cc_start: 0.0674 (mmp) cc_final: 0.0066 (ppp)
  outliers start: 28
  outliers final: 16
  residues processed: 107
  average time/residue: 0.3388
  time to fit residues: 54.0705
Evaluate side-chains
  106 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  405 PHE
Chi-restraints excluded: chain A residue  430 TYR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1326 TYR
Chi-restraints excluded: chain A residue 1331 ILE
Chi-restraints excluded: chain A residue 1338 SER
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   31 ILE
Chi-restraints excluded: chain C residue   54 LYS
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 33 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 99 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 150 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 138 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5067 r_free = 0.5067 target = 0.263955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.233994 restraints weight = 32141.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.237324 restraints weight = 19042.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.239105 restraints weight = 11534.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1856
moved from start:          1.0289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14414  Z= 0.137
  Angle     :  0.654  11.040  20059  Z= 0.329
  Chirality :  0.040   0.214   2356
  Planarity :  0.005   0.095   2153
  Dihedral  : 19.425 172.135   3326
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.33 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.21), residues: 1447
  helix:  0.15 (0.20), residues: 695
  sheet: -1.29 (0.50), residues: 98
  loop : -1.89 (0.22), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 476 
 HIS   0.013   0.002   HIS A1241 
 PHE   0.020   0.002   PHE A 491 
 TYR   0.024   0.002   TYR A 656 
 ARG   0.006   0.001   ARG A1122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04671 (  567)
  hydrogen bonds       : angle       4.71778 ( 1540)
  covalent geometry    : bond        0.00279 (14413)
  covalent geometry    : angle       0.65367 (20059)
  Misc. bond           : bond        0.00057 (    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
  108 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.1547 (OUTLIER) cc_final: -0.0187 (m-80)
REVERT: A  252 PHE cc_start: 0.1013 (OUTLIER) cc_final: 0.0246 (m-80)
REVERT: A  264 LEU cc_start: 0.4471 (tp) cc_final: 0.4258 (tp)
REVERT: A  379 ILE cc_start: 0.6153 (mm) cc_final: 0.5515 (mt)
REVERT: A  631 MET cc_start: -0.1545 (mmm) cc_final: -0.1918 (mmm)
REVERT: A  904 GLU cc_start: 0.6171 (tt0) cc_final: 0.4934 (mt-10)
REVERT: A  939 MET cc_start: -0.1596 (ptt) cc_final: -0.1835 (ttp)
REVERT: A  970 PHE cc_start: 0.3267 (m-80) cc_final: 0.2601 (m-80)
REVERT: A  976 ARG cc_start: 0.3330 (ptp-170) cc_final: 0.0203 (ptt-90)
REVERT: A 1056 GLU cc_start: 0.2291 (mt-10) cc_final: 0.1508 (tp30)
REVERT: A 1060 ARG cc_start: 0.3229 (mtp85) cc_final: 0.2451 (tpt90)
REVERT: C   30 LEU cc_start: -0.2509 (OUTLIER) cc_final: -0.3226 (tp)
REVERT: C   37 ASP cc_start: 0.6551 (t70) cc_final: 0.6035 (m-30)
REVERT: C   54 LYS cc_start: -0.1422 (OUTLIER) cc_final: -0.1786 (tmtt)
REVERT: C   77 MET cc_start: 0.0531 (mmp) cc_final: -0.0091 (ppp)
REVERT: C   79 THR cc_start: 0.0919 (p) cc_final: -0.1051 (m)
  outliers start: 19
  outliers final: 12
  residues processed: 103
  average time/residue: 0.3054
  time to fit residues: 46.0029
Evaluate side-chains
  102 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 TYR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  430 TYR
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1131 TYR
Chi-restraints excluded: chain A residue 1326 TYR
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   54 LYS
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 133 optimal weight:    0.5980
   chunk 104 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 69 optimal weight:    0.1980
   chunk 46 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    9.9990
   chunk 78 optimal weight:    0.0670
   chunk 131 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
A 255 ASN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5058 r_free = 0.5058 target = 0.262655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.228972 restraints weight = 32346.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.233758 restraints weight = 18191.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.236793 restraints weight = 11807.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.4820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1704
moved from start:          1.0318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  14414  Z= 0.104
  Angle     :  0.579  10.536  20059  Z= 0.288
  Chirality :  0.038   0.198   2356
  Planarity :  0.004   0.079   2153
  Dihedral  : 19.196 175.893   3326
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.83 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.22), residues: 1447
  helix:  0.47 (0.20), residues: 695
  sheet: -1.12 (0.52), residues: 98
  loop : -1.77 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A1241 
 PHE   0.011   0.001   PHE A 491 
 TYR   0.020   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 (  567)
  hydrogen bonds       : angle       4.30167 ( 1540)
  covalent geometry    : bond        0.00209 (14413)
  covalent geometry    : angle       0.57899 (20059)
  Misc. bond           : bond        0.00028 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5334.65 seconds
wall clock time: 95 minutes 4.98 seconds (5704.98 seconds total)