Starting phenix.real_space_refine
on Tue May 20 03:29:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sx7_40826/05_2025/8sx7_40826_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sx7_40826/05_2025/8sx7_40826.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sx7_40826/05_2025/8sx7_40826.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sx7_40826/05_2025/8sx7_40826.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sx7_40826/05_2025/8sx7_40826_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sx7_40826/05_2025/8sx7_40826_trim.cif"
  }
  resolution = 2.7
  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=   0.002 sd=   0.066
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
     S      38      5.16       5
     C    6177      2.51       5
     N    1602      2.21       5
     O    1701      1.98       5
     H    9719      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 19237
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 19203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1188, 19203
          Classifications: {'peptide': 1188}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1151}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {'ZWY': 1}
          Classifications: {'undetermined': 1, 'water': 3}
          Link IDs: {None: 3}
  Time building chain proxies: 9.81, per 1000 atoms: 0.51
  Number of scatterers: 19237
  At special positions: 0
  Unit cell: (84.335, 94.355, 144.455, 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      38     16.00
     O    1701      8.00
     N    1602      7.00
     C    6177      6.00
     H    9719      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.59
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2246

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 4 sheets defined
      71.5% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 17 through 24
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.807A  pdb=" N   GLU A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 95
      removed outlier: 3.623A  pdb=" N   ALA A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 122
      Proline residue:  A 110  - end of helix
      removed outlier: 3.652A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 179
      removed outlier: 3.532A  pdb=" N   LEU A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 190 through 201
      removed outlier: 3.637A  pdb=" N   LEU A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 212
      removed outlier: 3.968A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ILE A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   PHE A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 233
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 236 through 290
      removed outlier: 4.096A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
      removed outlier: 4.128A  pdb=" N   ALA A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   ARG A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ILE A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 326
    Processing helix  chain 'A' and resid 326 through 342
    Processing helix  chain 'A' and resid 347 through 367
    Processing helix  chain 'A' and resid 367 through 391
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 513 through 520
    Processing helix  chain 'A' and resid 522 through 526
    Processing helix  chain 'A' and resid 536 through 552
      removed outlier: 3.592A  pdb=" N   ALA A 548 " --> pdb=" O   ASN A 544 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP A 552 " --> pdb=" O   ALA A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 697 through 709
      removed outlier: 3.640A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 708 " --> pdb=" O   TYR A 704 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 709 " --> pdb=" O   PHE A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 745
      removed outlier: 3.596A  pdb=" N   ILE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 745 " --> pdb=" O   GLN A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 808
      removed outlier: 3.741A  pdb=" N   PHE A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 815
      removed outlier: 3.931A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 834
      removed outlier: 3.784A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 825 " --> pdb=" O   ILE A 821 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ILE A 829 " --> pdb=" O   PHE A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 861
      removed outlier: 3.766A  pdb=" N   LEU A 838 " --> pdb=" O   ASP A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 910
      Proline residue:  A 870  - end of helix
      removed outlier: 4.180A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
      Proline residue:  A 899  - end of helix
    Processing helix  chain 'A' and resid 910 through 917
    Processing helix  chain 'A' and resid 919 through 970
    Processing helix  chain 'A' and resid 971 through 974
    Processing helix  chain 'A' and resid 975 through 1015
      removed outlier: 4.064A  pdb=" N   MET A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU A1015 " --> pdb=" O   GLU A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1019
      removed outlier: 4.116A  pdb=" N   LEU A1019 " --> pdb=" O   TYR A1016 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1016 through 1019'
    Processing helix  chain 'A' and resid 1080 through 1089
      removed outlier: 3.535A  pdb=" N   ILE A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1108
      No H-bonds generated for 'chain 'A' and resid 1106 through 1108'
    Processing helix  chain 'A' and resid 1109 through 1116
      removed outlier: 3.737A  pdb=" N   LEU A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LYS A1116 " --> pdb=" O   ASP A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1155 through 1162
    Processing helix  chain 'A' and resid 1164 through 1168
    Processing helix  chain 'A' and resid 1178 through 1193
    Processing helix  chain 'A' and resid 1208 through 1223
      removed outlier: 4.309A  pdb=" N   LEU A1214 " --> pdb=" O   ARG A1210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing helix  chain 'A' and resid 1257 through 1264
      removed outlier: 3.549A  pdb=" N   ASN A1264 " --> pdb=" O   VAL A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1267 through 1277
      removed outlier: 3.631A  pdb=" N   LEU A1276 " --> pdb=" O   MET A1272 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A1277 " --> pdb=" O   VAL A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435
      removed outlier: 6.431A  pdb=" N   GLN A 429 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   THR A 416 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   LEU A 431 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE A 415 " --> pdb=" O   GLN A 466 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLN A 466 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.845A  pdb=" N   TYR A 556 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   VAL A 590 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU A 558 " --> pdb=" O   VAL A 590 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ILE A 603 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LYS A 614 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ILE A 605 " --> pdb=" O   VAL A 612 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 6.625A  pdb=" N   LYS A1059 " --> pdb=" O   ASN A1047 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ASN A1047 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   LEU A1061 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   PHE A1043 " --> pdb=" O   TRP A1099 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   TRP A1099 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ASN A1045 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   LYS A1097 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 6.386A  pdb=" N   SER A1118 " --> pdb=" O   ILE A1199 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   ASP A1201 " --> pdb=" O   SER A1118 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ILE A1120 " --> pdb=" O   ASP A1201 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LEU A1198 " --> pdb=" O   LEU A1229 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   ILE A1231 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE A1200 " --> pdb=" O   ILE A1231 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LYS A1070 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   MET A1245 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU A1254 " --> pdb=" O   VAL A1246 " (cutoff:3.500A)

    640 hydrogen bonds defined for protein.
    1875 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.98

  Time building geometry restraints manager: 6.53 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9705
        1.03 -     1.23: 24
        1.23 -     1.42: 4023
        1.42 -     1.62: 5629
        1.62 -     1.81: 60
  Bond restraints: 19441
  Sorted by residual:
  bond pdb=" C18 ZWY A1401 "
       pdb=" O20 ZWY A1401 "
    ideal  model  delta    sigma   weight residual
    1.452  1.324  0.128 2.00e-02 2.50e+03 4.08e+01
  bond pdb=" C08 ZWY A1401 "
       pdb=" C09 ZWY A1401 "
    ideal  model  delta    sigma   weight residual
    1.541  1.438  0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" C12 ZWY A1401 "
       pdb=" C13 ZWY A1401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.411  0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C01 ZWY A1401 "
       pdb=" C02 ZWY A1401 "
    ideal  model  delta    sigma   weight residual
    1.547  1.462  0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C03 ZWY A1401 "
       pdb=" C04 ZWY A1401 "
    ideal  model  delta    sigma   weight residual
    1.535  1.457  0.078 2.00e-02 2.50e+03 1.53e+01
  ... (remaining 19436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 33760
        1.50 -     3.00: 1336
        3.00 -     4.49: 82
        4.49 -     5.99: 13
        5.99 -     7.49: 6
  Bond angle restraints: 35197
  Sorted by residual:
  angle pdb=" CA  TRP A 947 "
        pdb=" CB  TRP A 947 "
        pdb=" CG  TRP A 947 "
      ideal   model   delta    sigma   weight residual
     113.60  119.34   -5.74 1.90e+00 2.77e-01 9.12e+00
  angle pdb=" C14 ZWY A1401 "
        pdb=" C19 ZWY A1401 "
        pdb=" C18 ZWY A1401 "
      ideal   model   delta    sigma   weight residual
     111.99  119.48   -7.49 3.00e+00 1.11e-01 6.23e+00
  angle pdb=" C   LEU A 582 "
        pdb=" N   HIS A 583 "
        pdb=" CA  HIS A 583 "
      ideal   model   delta    sigma   weight residual
     120.54  123.90   -3.36 1.35e+00 5.49e-01 6.19e+00
  angle pdb=" C04 ZWY A1401 "
        pdb=" C05 ZWY A1401 "
        pdb=" C15 ZWY A1401 "
      ideal   model   delta    sigma   weight residual
     112.74  120.14   -7.40 3.00e+00 1.11e-01 6.08e+00
  angle pdb=" CB  LYS A 375 "
        pdb=" CG  LYS A 375 "
        pdb=" CD  LYS A 375 "
      ideal   model   delta    sigma   weight residual
     111.30  116.96   -5.66 2.30e+00 1.89e-01 6.06e+00
  ... (remaining 35192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 8360
       17.48 -    34.96: 421
       34.96 -    52.44: 162
       52.44 -    69.92: 136
       69.92 -    87.40: 20
  Dihedral angle restraints: 9099
    sinusoidal: 4953
      harmonic: 4146
  Sorted by residual:
  dihedral pdb=" CA  ASP A  43 "
           pdb=" C   ASP A  43 "
           pdb=" N   MET A  44 "
           pdb=" CA  MET A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.76  -26.24     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  LYS A 585 "
           pdb=" C   LYS A 585 "
           pdb=" N   ILE A 586 "
           pdb=" CA  ILE A 586 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.73   25.27     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  ALA A1232 "
           pdb=" C   ALA A1232 "
           pdb=" N   HIS A1233 "
           pdb=" CA  HIS A1233 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.50   23.50     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 9096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.140: 1501
       0.140 -    0.280: 19
       0.280 -    0.420: 0
       0.420 -    0.561: 0
       0.561 -    0.701: 4
  Chirality restraints: 1524
  Sorted by residual:
  chirality pdb=" C05 ZWY A1401 "
            pdb=" C04 ZWY A1401 "
            pdb=" C06 ZWY A1401 "
            pdb=" C15 ZWY A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -1.76   -0.70 2.00e-01 2.50e+01 1.23e+01
  chirality pdb=" C06 ZWY A1401 "
            pdb=" C05 ZWY A1401 "
            pdb=" C07 ZWY A1401 "
            pdb=" C12 ZWY A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.71    2.08    0.62 2.00e-01 2.50e+01 9.75e+00
  chirality pdb=" C18 ZWY A1401 "
            pdb=" C17 ZWY A1401 "
            pdb=" C19 ZWY A1401 "
            pdb=" O20 ZWY A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -1.92   -0.62 2.00e-01 2.50e+01 9.71e+00
  ... (remaining 1521 not shown)

  Planarity restraints: 2787
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 587 "    0.270 9.50e-02 1.11e+02   9.99e-02 5.08e+01
        pdb=" NE  ARG A 587 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 587 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 587 "    0.028 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 587 "   -0.085 2.00e-02 2.50e+03
        pdb="HH11 ARG A 587 "    0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A 587 "   -0.040 2.00e-02 2.50e+03
        pdb="HH21 ARG A 587 "   -0.003 2.00e-02 2.50e+03
        pdb="HH22 ARG A 587 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  52 "   -0.184 9.50e-02 1.11e+02   6.76e-02 2.23e+01
        pdb=" NE  ARG A  52 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  52 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  52 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  52 "    0.054 2.00e-02 2.50e+03
        pdb="HH11 ARG A  52 "    0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A  52 "    0.028 2.00e-02 2.50e+03
        pdb="HH21 ARG A  52 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A  52 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 167 "   -0.141 9.50e-02 1.11e+02   5.13e-02 1.15e+01
        pdb=" NE  ARG A 167 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 167 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 167 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 167 "    0.042 2.00e-02 2.50e+03
        pdb="HH11 ARG A 167 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A 167 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 167 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 167 "   -0.041 2.00e-02 2.50e+03
  ... (remaining 2784 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 434
        2.11 -     2.73: 33830
        2.73 -     3.35: 57112
        3.35 -     3.98: 70667
        3.98 -     4.60: 113395
  Nonbonded interactions: 275438
  Sorted by model distance:
  nonbonded pdb=" HZ1 LYS A 177 "
            pdb=" OE1 GLU A 394 "
     model   vdw
     1.483 2.450
  nonbonded pdb=" O   LEU A 367 "
            pdb=" HG  SER A 371 "
     model   vdw
     1.535 2.450
  nonbonded pdb=" O   PHE A 333 "
            pdb=" HG1 THR A 337 "
     model   vdw
     1.551 2.450
  nonbonded pdb=" O   ALA A 296 "
            pdb=" HG1 THR A 300 "
     model   vdw
     1.571 2.450
  nonbonded pdb=" OD1 ASP A 842 "
            pdb=" H1  HOH A1501 "
     model   vdw
     1.590 2.450
  ... (remaining 275433 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.200
  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:             0.390
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.140
  Set scattering table:                    0.190
  Process input model:                     43.140
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
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      :  0.005   0.128   9722  Z= 0.254
  Angle     :  0.699   7.488  13184  Z= 0.393
  Chirality :  0.059   0.701   1524
  Planarity :  0.006   0.088   1639
  Dihedral  : 12.399  87.396   3596
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.81 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.21), residues: 1180
  helix: -1.18 (0.16), residues: 764
  sheet:  0.39 (0.63), residues: 51
  loop : -0.26 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 734 
 HIS   0.020   0.002   HIS A 153 
 PHE   0.022   0.002   PHE A 156 
 TYR   0.025   0.003   TYR A 123 
 ARG   0.016   0.002   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14719 (  640)
  hydrogen bonds       : angle       7.02453 ( 1875)
  covalent geometry    : bond        0.00537 ( 9722)
  covalent geometry    : angle       0.69852 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 211
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 ARG cc_start: 0.6690 (mtt-85) cc_final: 0.6363 (mmp80)
REVERT: A 1045 ASN cc_start: 0.7853 (t0) cc_final: 0.7286 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 215
  average time/residue: 2.0871
  time to fit residues: 490.0360
Evaluate side-chains
  110 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue 1248 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A 725 GLN
A 742 GLN
A1111 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.214020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.144763 restraints weight = 33729.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.41
r_work: 0.3667 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9722  Z= 0.222
  Angle     :  0.682   7.707  13184  Z= 0.367
  Chirality :  0.043   0.150   1524
  Planarity :  0.005   0.075   1639
  Dihedral  :  6.043  89.934   1352
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  :  9.97 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.23), residues: 1180
  helix:  0.14 (0.17), residues: 778
  sheet:  0.41 (0.64), residues: 55
  loop :  0.35 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 483 
 HIS   0.011   0.002   HIS A 153 
 PHE   0.019   0.002   PHE A 941 
 TYR   0.017   0.002   TYR A 764 
 ARG   0.011   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06209 (  640)
  hydrogen bonds       : angle       5.07843 ( 1875)
  covalent geometry    : bond        0.00473 ( 9722)
  covalent geometry    : angle       0.68191 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ASP cc_start: 0.7146 (m-30) cc_final: 0.6907 (m-30)
REVERT: A  121 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6444 (tm-30)
REVERT: A  319 MET cc_start: 0.7896 (mmm) cc_final: 0.7678 (mmt)
REVERT: A  347 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6987 (p)
REVERT: A  834 ASP cc_start: 0.7514 (t0) cc_final: 0.7179 (t70)
REVERT: A  884 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6884 (tm-30)
REVERT: A  921 GLN cc_start: 0.5044 (pm20) cc_final: 0.4636 (pt0)
REVERT: A 1045 ASN cc_start: 0.8213 (t0) cc_final: 0.7618 (t0)
REVERT: A 1116 LYS cc_start: 0.7669 (mmpt) cc_final: 0.7013 (mppt)
REVERT: A 1131 MET cc_start: 0.6455 (tpp) cc_final: 0.6233 (tpt)
REVERT: A 1166 MET cc_start: 0.5046 (OUTLIER) cc_final: 0.4764 (ptt)
  outliers start: 29
  outliers final: 8
  residues processed: 124
  average time/residue: 1.9798
  time to fit residues: 270.1466
Evaluate side-chains
  84 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue 1018 ASP
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1166 MET
Chi-restraints excluded: chain A residue 1204 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:   20.0000
   chunk 76 optimal weight:    1.9990
   chunk 39 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 113 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 193 GLN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 725 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.204006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131790 restraints weight = 33546.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.35
r_work: 0.3502 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.6968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   9722  Z= 0.282
  Angle     :  0.696   7.302  13184  Z= 0.376
  Chirality :  0.045   0.168   1524
  Planarity :  0.005   0.056   1639
  Dihedral  :  5.857  80.589   1349
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 11.23 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.23), residues: 1180
  helix:  0.46 (0.18), residues: 772
  sheet:  0.07 (0.57), residues: 60
  loop :  0.41 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  89 
 HIS   0.015   0.002   HIS A 153 
 PHE   0.028   0.002   PHE A 352 
 TYR   0.021   0.002   TYR A 881 
 ARG   0.007   0.001   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07169 (  640)
  hydrogen bonds       : angle       4.97759 ( 1875)
  covalent geometry    : bond        0.00663 ( 9722)
  covalent geometry    : angle       0.69562 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7123 (m-30)
REVERT: A  284 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7902 (mtt90)
REVERT: A  763 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.7543 (t60)
REVERT: A  801 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8389 (ttm)
REVERT: A  868 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7731 (tt)
REVERT: A 1045 ASN cc_start: 0.8479 (t0) cc_final: 0.7990 (t0)
REVERT: A 1122 GLN cc_start: 0.8107 (tt0) cc_final: 0.7845 (tt0)
REVERT: A 1133 LYS cc_start: 0.5348 (mmtt) cc_final: 0.4921 (tmtm)
REVERT: A 1166 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.4486 (ppp)
  outliers start: 37
  outliers final: 13
  residues processed: 106
  average time/residue: 2.0378
  time to fit residues: 237.4596
Evaluate side-chains
  87 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  763 TRP
Chi-restraints excluded: chain A residue  801 MET
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1018 ASP
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1157 GLU
Chi-restraints excluded: chain A residue 1166 MET
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1228 VAL
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.206376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.139397 restraints weight = 33808.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 3.69
r_work: 0.3508 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.7322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9722  Z= 0.148
  Angle     :  0.531   7.024  13184  Z= 0.285
  Chirality :  0.039   0.145   1524
  Planarity :  0.004   0.049   1639
  Dihedral  :  5.173  70.681   1349
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.17 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.24), residues: 1180
  helix:  1.17 (0.18), residues: 777
  sheet: -0.19 (0.55), residues: 64
  loop :  0.73 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 947 
 HIS   0.009   0.001   HIS A 153 
 PHE   0.014   0.001   PHE A 939 
 TYR   0.016   0.001   TYR A 728 
 ARG   0.005   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05588 (  640)
  hydrogen bonds       : angle       4.43683 ( 1875)
  covalent geometry    : bond        0.00322 ( 9722)
  covalent geometry    : angle       0.53094 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6939 (m-30)
REVERT: A  284 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7955 (mtt90)
REVERT: A  801 MET cc_start: 0.8555 (ttp) cc_final: 0.8230 (ttm)
REVERT: A  868 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7727 (tt)
REVERT: A  884 GLU cc_start: 0.7646 (tt0) cc_final: 0.7430 (tt0)
REVERT: A 1045 ASN cc_start: 0.8480 (t0) cc_final: 0.8028 (t0)
REVERT: A 1084 LEU cc_start: 0.7242 (pp) cc_final: 0.6867 (tp)
REVERT: A 1133 LYS cc_start: 0.5386 (mmtt) cc_final: 0.4886 (tmtm)
REVERT: A 1202 GLU cc_start: 0.4262 (tm-30) cc_final: 0.3992 (tm-30)
  outliers start: 26
  outliers final: 14
  residues processed: 93
  average time/residue: 1.8543
  time to fit residues: 191.8094
Evaluate side-chains
  88 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  886 SER
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1228 VAL
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1256 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 106 optimal weight:    7.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.203677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.131495 restraints weight = 33972.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.40
r_work: 0.3508 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.7761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9722  Z= 0.181
  Angle     :  0.556   6.593  13184  Z= 0.302
  Chirality :  0.040   0.160   1524
  Planarity :  0.004   0.050   1639
  Dihedral  :  5.296  76.517   1349
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.13 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.24), residues: 1180
  helix:  1.29 (0.18), residues: 769
  sheet:  0.08 (0.61), residues: 55
  loop :  0.54 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 947 
 HIS   0.011   0.002   HIS A 153 
 PHE   0.023   0.002   PHE A 352 
 TYR   0.015   0.002   TYR A 728 
 ARG   0.003   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05928 (  640)
  hydrogen bonds       : angle       4.41437 ( 1875)
  covalent geometry    : bond        0.00412 ( 9722)
  covalent geometry    : angle       0.55649 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 1.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.6817 (mppt) cc_final: 0.6384 (ttpt)
REVERT: A  241 MET cc_start: 0.8131 (mmt) cc_final: 0.7876 (mmt)
REVERT: A  270 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6990 (m-30)
REVERT: A  284 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7946 (mtt90)
REVERT: A  763 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.7392 (t60)
REVERT: A  801 MET cc_start: 0.8559 (ttp) cc_final: 0.8271 (ttm)
REVERT: A 1045 ASN cc_start: 0.8539 (t0) cc_final: 0.8107 (t0)
REVERT: A 1084 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7213 (tp)
REVERT: A 1133 LYS cc_start: 0.5305 (mmtt) cc_final: 0.4760 (tmtm)
REVERT: A 1183 GLN cc_start: 0.7865 (mt0) cc_final: 0.7648 (mt0)
  outliers start: 29
  outliers final: 21
  residues processed: 93
  average time/residue: 1.7509
  time to fit residues: 182.2583
Evaluate side-chains
  97 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 1.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  763 TRP
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  886 SER
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1084 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1157 GLU
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1228 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1256 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 116 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 85 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.204118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.132206 restraints weight = 33942.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.41
r_work: 0.3519 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.8046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9722  Z= 0.156
  Angle     :  0.516   6.578  13184  Z= 0.279
  Chirality :  0.039   0.154   1524
  Planarity :  0.004   0.048   1639
  Dihedral  :  5.053  73.691   1349
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.62 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.24), residues: 1180
  helix:  1.52 (0.19), residues: 770
  sheet:  0.03 (0.60), residues: 55
  loop :  0.56 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 947 
 HIS   0.008   0.001   HIS A 153 
 PHE   0.014   0.001   PHE A 939 
 TYR   0.014   0.001   TYR A 728 
 ARG   0.002   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05558 (  640)
  hydrogen bonds       : angle       4.25340 ( 1875)
  covalent geometry    : bond        0.00343 ( 9722)
  covalent geometry    : angle       0.51571 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6931 (m-30)
REVERT: A  801 MET cc_start: 0.8534 (ttp) cc_final: 0.8272 (ttm)
REVERT: A 1045 ASN cc_start: 0.8558 (t0) cc_final: 0.8142 (t0)
REVERT: A 1084 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7364 (tp)
REVERT: A 1133 LYS cc_start: 0.5341 (mmtt) cc_final: 0.4833 (tmtm)
  outliers start: 25
  outliers final: 19
  residues processed: 88
  average time/residue: 1.7438
  time to fit residues: 171.4554
Evaluate side-chains
  93 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1084 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1201 ASP
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 116 optimal weight:    3.9990
   chunk 76 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 117 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
A1139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.204306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.132800 restraints weight = 33855.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.41
r_work: 0.3526 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.8225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9722  Z= 0.139
  Angle     :  0.503   6.727  13184  Z= 0.270
  Chirality :  0.038   0.146   1524
  Planarity :  0.004   0.050   1639
  Dihedral  :  4.940  73.541   1349
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.71 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.25), residues: 1180
  helix:  1.71 (0.19), residues: 770
  sheet:  0.13 (0.61), residues: 55
  loop :  0.57 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 947 
 HIS   0.014   0.001   HIS A  35 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.013   0.001   TYR A 728 
 ARG   0.009   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05341 (  640)
  hydrogen bonds       : angle       4.15686 ( 1875)
  covalent geometry    : bond        0.00300 ( 9722)
  covalent geometry    : angle       0.50257 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6967 (m-30)
REVERT: A  284 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7897 (ttm170)
REVERT: A  801 MET cc_start: 0.8505 (ttp) cc_final: 0.8257 (ttm)
REVERT: A 1045 ASN cc_start: 0.8548 (t0) cc_final: 0.8136 (t0)
REVERT: A 1133 LYS cc_start: 0.5333 (mmtt) cc_final: 0.4836 (tmtm)
  outliers start: 22
  outliers final: 20
  residues processed: 94
  average time/residue: 1.7466
  time to fit residues: 183.5293
Evaluate side-chains
  94 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  886 SER
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1097 LYS
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1256 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:   20.0000
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.201521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.129818 restraints weight = 33826.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.37
r_work: 0.3485 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.8516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9722  Z= 0.202
  Angle     :  0.562   6.166  13184  Z= 0.306
  Chirality :  0.041   0.165   1524
  Planarity :  0.004   0.049   1639
  Dihedral  :  5.480  86.687   1349
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.62 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1180
  helix:  1.43 (0.18), residues: 769
  sheet: -0.29 (0.65), residues: 56
  loop :  0.38 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 947 
 HIS   0.011   0.002   HIS A  35 
 PHE   0.020   0.002   PHE A 156 
 TYR   0.016   0.002   TYR A 728 
 ARG   0.004   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06114 (  640)
  hydrogen bonds       : angle       4.37276 ( 1875)
  covalent geometry    : bond        0.00464 ( 9722)
  covalent geometry    : angle       0.56238 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6957 (m-30)
REVERT: A  284 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7949 (ttm170)
REVERT: A  763 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7436 (t60)
REVERT: A 1045 ASN cc_start: 0.8577 (t0) cc_final: 0.8174 (t0)
REVERT: A 1183 GLN cc_start: 0.7527 (mt0) cc_final: 0.7288 (mp10)
  outliers start: 28
  outliers final: 19
  residues processed: 88
  average time/residue: 1.6725
  time to fit residues: 165.0124
Evaluate side-chains
  92 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  763 TRP
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  886 SER
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 112 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:   20.0000
   chunk 13 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A1139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.204463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133808 restraints weight = 33757.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.39
r_work: 0.3533 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.8563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9722  Z= 0.120
  Angle     :  0.480   6.171  13184  Z= 0.257
  Chirality :  0.037   0.145   1524
  Planarity :  0.004   0.047   1639
  Dihedral  :  4.925  76.905   1349
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.59 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.25), residues: 1180
  helix:  1.84 (0.19), residues: 770
  sheet: -0.28 (0.64), residues: 58
  loop :  0.48 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 947 
 HIS   0.012   0.001   HIS A  35 
 PHE   0.014   0.001   PHE A 882 
 TYR   0.013   0.001   TYR A 728 
 ARG   0.006   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05185 (  640)
  hydrogen bonds       : angle       4.08879 ( 1875)
  covalent geometry    : bond        0.00247 ( 9722)
  covalent geometry    : angle       0.48013 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6930 (m-30)
REVERT: A  284 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7884 (ttm170)
REVERT: A 1045 ASN cc_start: 0.8516 (t0) cc_final: 0.8095 (t0)
REVERT: A 1183 GLN cc_start: 0.7603 (mt0) cc_final: 0.7392 (mp10)
  outliers start: 18
  outliers final: 16
  residues processed: 88
  average time/residue: 1.5480
  time to fit residues: 154.5669
Evaluate side-chains
  90 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  886 SER
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 56 optimal weight:   20.0000
   chunk 109 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.3544

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

Flipped N/Q/H residues before XYZ refinement:
A1139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.203221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132550 restraints weight = 33690.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.38
r_work: 0.3517 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.8685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9722  Z= 0.143
  Angle     :  0.499   5.464  13184  Z= 0.269
  Chirality :  0.038   0.147   1524
  Planarity :  0.004   0.048   1639
  Dihedral  :  5.061  81.098   1349
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.78 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.25), residues: 1180
  helix:  1.83 (0.19), residues: 770
  sheet:  0.34 (0.71), residues: 45
  loop :  0.36 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 947 
 HIS   0.007   0.001   HIS A  35 
 PHE   0.018   0.002   PHE A 882 
 TYR   0.013   0.001   TYR A 728 
 ARG   0.005   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05413 (  640)
  hydrogen bonds       : angle       4.11013 ( 1875)
  covalent geometry    : bond        0.00312 ( 9722)
  covalent geometry    : angle       0.49897 (13184)

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7005 (m-30)
REVERT: A  284 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7902 (ttm170)
REVERT: A 1045 ASN cc_start: 0.8524 (t0) cc_final: 0.8115 (t0)
REVERT: A 1136 ASP cc_start: 0.7009 (t0) cc_final: 0.6590 (t70)
REVERT: A 1183 GLN cc_start: 0.7480 (mt0) cc_final: 0.7257 (mp10)
  outliers start: 17
  outliers final: 16
  residues processed: 85
  average time/residue: 1.5627
  time to fit residues: 151.2724
Evaluate side-chains
  91 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  886 SER
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 6 optimal weight:    0.4980
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0010
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.2390

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

Flipped N/Q/H residues before XYZ refinement:
A 909 GLN
A1139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.203676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138938 restraints weight = 33996.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 3.42
r_work: 0.3501 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.8799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9722  Z= 0.133
  Angle     :  0.480   5.113  13184  Z= 0.258
  Chirality :  0.038   0.145   1524
  Planarity :  0.004   0.047   1639
  Dihedral  :  4.927  78.769   1349
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.88 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.25), residues: 1180
  helix:  1.93 (0.19), residues: 770
  sheet:  0.43 (0.71), residues: 45
  loop :  0.39 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 947 
 HIS   0.009   0.001   HIS A  35 
 PHE   0.018   0.001   PHE A 882 
 TYR   0.013   0.001   TYR A 728 
 ARG   0.005   0.000   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05248 (  640)
  hydrogen bonds       : angle       4.04062 ( 1875)
  covalent geometry    : bond        0.00285 ( 9722)
  covalent geometry    : angle       0.48032 (13184)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16229.53 seconds
wall clock time: 277 minutes 14.27 seconds (16634.27 seconds total)