Starting phenix.real_space_refine
on Fri Feb 14 04:18:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i4b_35168/02_2025/8i4b_35168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i4b_35168/02_2025/8i4b_35168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i4b_35168/02_2025/8i4b_35168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i4b_35168/02_2025/8i4b_35168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i4b_35168/02_2025/8i4b_35168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i4b_35168/02_2025/8i4b_35168.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.063
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: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    6316      2.51       5
     N    1637      2.21       5
     O    1731      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9727
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1218, 9727
          Classifications: {'peptide': 1218}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178}
          Chain breaks: 2
  Time building chain proxies: 5.83, per 1000 atoms: 0.60
  Number of scatterers: 9727
  At special positions: 0
  Unit cell: (77.04, 114.49, 149.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1731      8.00
     N    1637      7.00
     C    6316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.57
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2306

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 5 sheets defined
      66.7% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 18 through 23
      removed outlier: 3.797A  pdb=" N   PHE A  23 " --> pdb=" O   CYS A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 27 through 37
      removed outlier: 3.676A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 75
    Processing helix  chain 'A' and resid 79 through 93
      removed outlier: 5.379A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 121
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 128 through 150
    Processing helix  chain 'A' and resid 151 through 179
      removed outlier: 3.640A  pdb=" N   GLY A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 189
      removed outlier: 3.676A  pdb=" N   LYS A 188 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 4.476A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   HIS A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 218 through 233
      removed outlier: 3.586A  pdb=" N   ALA A 222 " --> pdb=" O   GLY A 218 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 246
      removed outlier: 3.536A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 248
      No H-bonds generated for 'chain 'A' and resid 247 through 248'
    Processing helix  chain 'A' and resid 249 through 253
    Processing helix  chain 'A' and resid 265 through 282
      removed outlier: 4.415A  pdb=" N   ALA A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
    Processing helix  chain 'A' and resid 291 through 342
      removed outlier: 4.154A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
      removed outlier: 3.550A  pdb=" N   VAL A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 390
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 512
      removed outlier: 3.552A  pdb=" N   VAL A 507 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 520
      removed outlier: 4.493A  pdb=" N   ASP A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 552
      removed outlier: 3.734A  pdb=" N   ASP A 552 " --> pdb=" O   ALA A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.567A  pdb=" N   SER A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 585
      removed outlier: 3.868A  pdb=" N   GLU A 584 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 600
      removed outlier: 3.573A  pdb=" N   TYR A 596 " --> pdb=" O   GLN A 593 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LYS A 598 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 623
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 698 through 709
      removed outlier: 3.759A  pdb=" N   ALA A 707 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY A 708 " --> pdb=" O   TYR A 704 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 709 " --> pdb=" O   PHE A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 744
      removed outlier: 3.917A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 806
      removed outlier: 3.500A  pdb=" N   TYR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 3.839A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN A 816 " --> pdb=" O   PHE A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 823
    Processing helix  chain 'A' and resid 827 through 835
      removed outlier: 3.662A  pdb=" N   ASP A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 861
      removed outlier: 3.573A  pdb=" N   ILE A 844 " --> pdb=" O   PHE A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 866
    Processing helix  chain 'A' and resid 869 through 884
      removed outlier: 3.632A  pdb=" N   ILE A 874 " --> pdb=" O   PRO A 870 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   PHE A 875 " --> pdb=" O   LEU A 871 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A 876 " --> pdb=" O   GLY A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 910
      removed outlier: 3.880A  pdb=" N   PHE A 901 " --> pdb=" O   ARG A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 917
      removed outlier: 3.630A  pdb=" N   TYR A 917 " --> pdb=" O   THR A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 932
    Processing helix  chain 'A' and resid 936 through 967
      removed outlier: 3.855A  pdb=" N   LEU A 940 " --> pdb=" O   GLU A 936 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER A 945 " --> pdb=" O   PHE A 941 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG A 951 " --> pdb=" O   TRP A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1017
      removed outlier: 4.254A  pdb=" N   MET A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1089
      removed outlier: 4.054A  pdb=" N   SER A1086 " --> pdb=" O   SER A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1108
    Processing helix  chain 'A' and resid 1109 through 1113
    Processing helix  chain 'A' and resid 1130 through 1136
      removed outlier: 3.563A  pdb=" N   LEU A1135 " --> pdb=" O   MET A1131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1155 through 1160
    Processing helix  chain 'A' and resid 1178 through 1194
    Processing helix  chain 'A' and resid 1208 through 1223
      removed outlier: 3.681A  pdb=" N   PHE A1223 " --> pdb=" O   ILE A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1264
      removed outlier: 3.727A  pdb=" N   ASN A1264 " --> pdb=" O   VAL A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1267 through 1277
      removed outlier: 3.720A  pdb=" N   LEU A1276 " --> pdb=" O   MET A1272 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLY A1277 " --> pdb=" O   VAL A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1278 through 1297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435
      removed outlier: 3.905A  pdb=" N   PHE A 415 " --> pdb=" O   HIS A 466 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   HIS 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: 6.447A  pdb=" N   THR A 587 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   VAL A 443 " --> pdb=" O   THR A 587 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU A 589 " --> pdb=" O   VAL A 443 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLN A 602 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 606 " --> pdb=" O   VAL A 444 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLN A 613 " --> pdb=" O   ILE A 605 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LYS A 607 " --> pdb=" O   MET A 611 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   MET A 611 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488
      removed outlier: 3.651A  pdb=" N   GLY A 487 " --> pdb=" O   ILE A 528 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 6.921A  pdb=" N   LYS A1059 " --> pdb=" O   ASN A1047 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ASN A1047 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   LEU A1061 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   PHE A1043 " --> pdb=" O   TRP A1099 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   TRP A1099 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   ASN A1045 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LYS A1097 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120
      removed outlier: 6.490A  pdb=" N   VAL A1071 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   LYS A1070 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   MET A1245 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   ILE A1244 " --> pdb=" O   TYR A1255 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   TYR A1255 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL A1246 " --> pdb=" O   LYS A1253 " (cutoff:3.500A)

    571 hydrogen bonds defined for protein.
    1653 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: 3.64

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1654
        1.32 -     1.44: 2578
        1.44 -     1.56: 5633
        1.56 -     1.69: 1
        1.69 -     1.81: 70
  Bond restraints: 9936
  Sorted by residual:
  bond pdb=" CB  ARG A 782 "
       pdb=" CG  ARG A 782 "
    ideal  model  delta    sigma   weight residual
    1.520  1.409  0.111 3.00e-02 1.11e+03 1.38e+01
  bond pdb=" CB  GLN A 845 "
       pdb=" CG  GLN A 845 "
    ideal  model  delta    sigma   weight residual
    1.520  1.422  0.098 3.00e-02 1.11e+03 1.06e+01
  bond pdb=" CB  VAL A 159 "
       pdb=" CG1 VAL A 159 "
    ideal  model  delta    sigma   weight residual
    1.521  1.415  0.106 3.30e-02 9.18e+02 1.03e+01
  bond pdb=" CB  ILE A 331 "
       pdb=" CG2 ILE A 331 "
    ideal  model  delta    sigma   weight residual
    1.521  1.418  0.103 3.30e-02 9.18e+02 9.82e+00
  bond pdb=" CB  THR A  99 "
       pdb=" CG2 THR A  99 "
    ideal  model  delta    sigma   weight residual
    1.521  1.420  0.101 3.30e-02 9.18e+02 9.33e+00
  ... (remaining 9931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 13079
        2.77 -     5.54: 336
        5.54 -     8.31: 37
        8.31 -    11.08: 8
       11.08 -    13.85: 3
  Bond angle restraints: 13463
  Sorted by residual:
  angle pdb=" CB  MET A 990 "
        pdb=" CG  MET A 990 "
        pdb=" SD  MET A 990 "
      ideal   model   delta    sigma   weight residual
     112.70  126.55  -13.85 3.00e+00 1.11e-01 2.13e+01
  angle pdb=" CG1 ILE A 147 "
        pdb=" CB  ILE A 147 "
        pdb=" CG2 ILE A 147 "
      ideal   model   delta    sigma   weight residual
     110.70   97.12   13.58 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C   ARG A1220 "
        pdb=" N   GLU A1221 "
        pdb=" CA  GLU A1221 "
      ideal   model   delta    sigma   weight residual
     122.56  115.53    7.03 1.72e+00 3.38e-01 1.67e+01
  angle pdb=" CG1 ILE A 805 "
        pdb=" CB  ILE A 805 "
        pdb=" CG2 ILE A 805 "
      ideal   model   delta    sigma   weight residual
     110.70   99.33   11.37 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" C   ASP A  43 "
        pdb=" N   MET A  44 "
        pdb=" CA  MET A  44 "
      ideal   model   delta    sigma   weight residual
     120.87  127.24   -6.37 1.69e+00 3.50e-01 1.42e+01
  ... (remaining 13458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 5346
       17.76 -    35.53: 499
       35.53 -    53.29: 79
       53.29 -    71.06: 11
       71.06 -    88.82: 6
  Dihedral angle restraints: 5941
    sinusoidal: 2382
      harmonic: 3559
  Sorted by residual:
  dihedral pdb=" CA  ASP A 975 "
           pdb=" C   ASP A 975 "
           pdb=" N   ALA A 976 "
           pdb=" CA  ALA A 976 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.62  -22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  SER A 252 "
           pdb=" C   SER A 252 "
           pdb=" N   CYS A 253 "
           pdb=" CA  CYS A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  ILE A 194 "
           pdb=" C   ILE A 194 "
           pdb=" N   VAL A 195 "
           pdb=" CA  VAL A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.49   20.51     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 5938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1316
       0.086 -    0.171: 230
       0.171 -    0.257: 12
       0.257 -    0.343: 2
       0.343 -    0.428: 1
  Chirality restraints: 1561
  Sorted by residual:
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.58e+00
  chirality pdb=" CB  VAL A 889 "
            pdb=" CA  VAL A 889 "
            pdb=" CG1 VAL A 889 "
            pdb=" CG2 VAL A 889 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CB  ILE A 346 "
            pdb=" CA  ILE A 346 "
            pdb=" CG1 ILE A 346 "
            pdb=" CG2 ILE A 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1558 not shown)

  Planarity restraints: 1673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 218 "    0.052 5.00e-02 4.00e+02   7.87e-02 9.92e+00
        pdb=" N   PRO A 219 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 219 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 219 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 109 "    0.049 5.00e-02 4.00e+02   7.44e-02 8.85e+00
        pdb=" N   PRO A 110 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 840 "   -0.027 2.00e-02 2.50e+03   2.11e-02 7.77e+00
        pdb=" CG  PHE A 840 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 840 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 840 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 840 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 840 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 840 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1670 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 745
        2.71 -     3.26: 9858
        3.26 -     3.80: 15696
        3.80 -     4.35: 19666
        4.35 -     4.90: 33704
  Nonbonded interactions: 79669
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 953 "
            pdb=" NE2 GLN A 994 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" O   THR A 488 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER A 479 "
            pdb=" O   GLN A 481 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ARG A 706 "
            pdb=" NH1 ARG A 706 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE2 GLU A1221 "
            pdb=" NZ  LYS A1222 "
     model   vdw
     2.218 3.120
  ... (remaining 79664 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=1.00 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:                  0.010
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.580
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
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      :  0.017   0.117   9936  Z= 1.053
  Angle     :  1.070  13.849  13463  Z= 0.581
  Chirality :  0.063   0.428   1561
  Planarity :  0.007   0.079   1673
  Dihedral  : 14.068  88.819   3635
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -2.17 (0.22), residues: 1212
  helix: -1.25 (0.17), residues: 795
  sheet: -0.48 (0.54), residues: 72
  loop : -1.68 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A  64 
 HIS   0.014   0.002   HIS A 153 
 PHE   0.046   0.004   PHE A 840 
 TYR   0.031   0.003   TYR A1016 
 ARG   0.012   0.001   ARG A 824 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  206 ASP cc_start: 0.8006 (m-30) cc_final: 0.7619 (m-30)
REVERT: A  319 MET cc_start: 0.8159 (tpp) cc_final: 0.7638 (mmt)
REVERT: A  345 VAL cc_start: 0.8308 (p) cc_final: 0.8074 (m)
REVERT: A  887 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6534 (mtt180)
REVERT: A 1135 LEU cc_start: 0.8577 (mp) cc_final: 0.7922 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2381
  time to fit residues: 40.0314
Evaluate side-chains
  91 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0770
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0370
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    0.4980
   chunk 70 optimal weight:    0.5980
   chunk 109 optimal weight:    0.0870
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
A 387 GLN
A 492 ASN
** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.252373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.191068 restraints weight = 10093.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 1.98
r_work: 0.3595 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9936  Z= 0.158
  Angle     :  0.538   8.005  13463  Z= 0.286
  Chirality :  0.039   0.141   1561
  Planarity :  0.005   0.052   1673
  Dihedral  :  4.613  17.505   1314
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.18 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -0.02 (0.24), residues: 1212
  helix:  0.41 (0.19), residues: 798
  sheet:  0.34 (0.58), residues: 64
  loop : -0.85 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A  35 
 PHE   0.022   0.002   PHE A 941 
 TYR   0.021   0.001   TYR A1016 
 ARG   0.004   0.001   ARG A 384 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7643 (tt0) cc_final: 0.7299 (mt-10)
REVERT: A  122 ASN cc_start: 0.8572 (m-40) cc_final: 0.8310 (m-40)
REVERT: A  147 ILE cc_start: 0.7937 (tt) cc_final: 0.7723 (tt)
REVERT: A  173 MET cc_start: 0.8163 (mtm) cc_final: 0.7881 (mtp)
REVERT: A  268 PHE cc_start: 0.7243 (m-10) cc_final: 0.6986 (m-80)
REVERT: A  345 VAL cc_start: 0.8441 (p) cc_final: 0.8169 (m)
REVERT: A  391 LEU cc_start: 0.8215 (mt) cc_final: 0.7966 (mt)
REVERT: A  717 LEU cc_start: 0.7706 (tp) cc_final: 0.7504 (tp)
REVERT: A  744 MET cc_start: 0.7357 (ptp) cc_final: 0.7092 (tmm)
REVERT: A  805 ILE cc_start: 0.8293 (tt) cc_final: 0.8031 (tt)
REVERT: A  887 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6841 (mtt180)
REVERT: A  922 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6916 (tmm-80)
REVERT: A 1015 GLU cc_start: 0.7026 (tp30) cc_final: 0.6458 (tt0)
REVERT: A 1018 ASP cc_start: 0.6831 (t70) cc_final: 0.6613 (t70)
  outliers start: 6
  outliers final: 2
  residues processed: 108
  average time/residue: 0.2436
  time to fit residues: 37.1184
Evaluate side-chains
  85 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue 1038 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 47 optimal weight:    0.4980
   chunk 79 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 72 optimal weight:    0.1980
   chunk 23 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 102 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  35 HIS
A 602 GLN
A 924 GLN
** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1154 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.251612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.189390 restraints weight = 10302.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 1.87
r_work: 0.3619 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9936  Z= 0.172
  Angle     :  0.496   6.124  13463  Z= 0.263
  Chirality :  0.039   0.155   1561
  Planarity :  0.004   0.050   1673
  Dihedral  :  4.082  16.259   1314
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.87 %
    Favored  : 92.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.77 (0.25), residues: 1212
  helix:  0.98 (0.19), residues: 805
  sheet:  0.46 (0.53), residues: 75
  loop : -0.45 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A 798 
 PHE   0.020   0.002   PHE A 336 
 TYR   0.011   0.001   TYR A 157 
 ARG   0.004   0.000   ARG A 384 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A   33 ILE cc_start: 0.7892 (mm) cc_final: 0.7544 (mt)
REVERT: A   70 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7643 (tmm160)
REVERT: A   89 TRP cc_start: 0.8054 (p-90) cc_final: 0.7696 (p-90)
REVERT: A  121 GLU cc_start: 0.7855 (tt0) cc_final: 0.7525 (mt-10)
REVERT: A  268 PHE cc_start: 0.7558 (m-10) cc_final: 0.7350 (m-80)
REVERT: A  345 VAL cc_start: 0.8632 (p) cc_final: 0.8352 (m)
REVERT: A  805 ILE cc_start: 0.8209 (tt) cc_final: 0.7884 (tt)
REVERT: A  887 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7498 (mtt90)
REVERT: A  922 ARG cc_start: 0.7298 (tpp80) cc_final: 0.6838 (tmm-80)
REVERT: A  926 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7937 (tt)
REVERT: A 1002 GLU cc_start: 0.7406 (tt0) cc_final: 0.6945 (mt-10)
REVERT: A 1005 ASN cc_start: 0.7121 (t0) cc_final: 0.6601 (m-40)
REVERT: A 1018 ASP cc_start: 0.7213 (t70) cc_final: 0.6938 (t0)
REVERT: A 1107 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7973 (mt-10)
REVERT: A 1135 LEU cc_start: 0.7851 (mp) cc_final: 0.7584 (mp)
  outliers start: 7
  outliers final: 4
  residues processed: 94
  average time/residue: 0.2377
  time to fit residues: 31.9673
Evaluate side-chains
  86 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1106 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 118 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.246969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.187423 restraints weight = 10120.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 2.11
r_work: 0.3479 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9936  Z= 0.278
  Angle     :  0.532   5.926  13463  Z= 0.280
  Chirality :  0.041   0.157   1561
  Planarity :  0.004   0.057   1673
  Dihedral  :  4.166  17.548   1314
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  8.76 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.72 (0.24), residues: 1212
  helix:  0.87 (0.19), residues: 800
  sheet:  0.37 (0.54), residues: 80
  loop : -0.22 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.005   0.001   HIS A 153 
 PHE   0.023   0.002   PHE A 336 
 TYR   0.013   0.001   TYR A 157 
 ARG   0.004   0.000   ARG A 262 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A   33 ILE cc_start: 0.7838 (mm) cc_final: 0.7633 (mt)
REVERT: A   58 GLU cc_start: 0.8074 (tt0) cc_final: 0.7346 (mm-30)
REVERT: A   89 TRP cc_start: 0.7967 (p-90) cc_final: 0.7756 (p-90)
REVERT: A  121 GLU cc_start: 0.7950 (tt0) cc_final: 0.7676 (mt-10)
REVERT: A  197 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7547 (pt)
REVERT: A  345 VAL cc_start: 0.8786 (p) cc_final: 0.8512 (m)
REVERT: A  887 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7446 (mtt180)
REVERT: A  922 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6948 (tmm-80)
REVERT: A  926 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8055 (tt)
REVERT: A 1018 ASP cc_start: 0.7412 (t70) cc_final: 0.7201 (t70)
REVERT: A 1107 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8225 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8228 (mp) cc_final: 0.7957 (mp)
REVERT: A 1155 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6370 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 98
  average time/residue: 0.2365
  time to fit residues: 33.0965
Evaluate side-chains
  93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  840 PHE
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1106 THR
Chi-restraints excluded: chain A residue 1155 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   chunk 54 optimal weight:   20.0000
   chunk 65 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 99 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.248438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.188759 restraints weight = 10048.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 2.03
r_work: 0.3545 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9936  Z= 0.223
  Angle     :  0.490   5.632  13463  Z= 0.259
  Chirality :  0.040   0.153   1561
  Planarity :  0.003   0.050   1673
  Dihedral  :  3.996  16.477   1314
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.79 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.95 (0.24), residues: 1212
  helix:  1.04 (0.19), residues: 805
  sheet:  0.45 (0.54), residues: 80
  loop : -0.10 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A 153 
 PHE   0.020   0.002   PHE A 336 
 TYR   0.012   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A 262 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A   33 ILE cc_start: 0.7813 (mm) cc_final: 0.7606 (mt)
REVERT: A   41 GLU cc_start: 0.8031 (mp0) cc_final: 0.7595 (mt-10)
REVERT: A  345 VAL cc_start: 0.8749 (p) cc_final: 0.8519 (m)
REVERT: A  763 TRP cc_start: 0.8672 (t60) cc_final: 0.8357 (t-100)
REVERT: A  887 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7438 (mtt180)
REVERT: A  926 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7898 (tp)
REVERT: A 1018 ASP cc_start: 0.7312 (t70) cc_final: 0.7111 (t70)
REVERT: A 1107 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8206 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8271 (mp) cc_final: 0.8020 (mp)
REVERT: A 1155 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6438 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 98
  average time/residue: 0.2206
  time to fit residues: 31.7818
Evaluate side-chains
  92 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  840 PHE
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1155 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 44 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0670
   chunk 91 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 104 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.251277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.187289 restraints weight = 10079.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 1.90
r_work: 0.3565 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9936  Z= 0.148
  Angle     :  0.459   9.128  13463  Z= 0.240
  Chirality :  0.039   0.146   1561
  Planarity :  0.003   0.047   1673
  Dihedral  :  3.790  14.793   1314
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.73 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.36 (0.25), residues: 1212
  helix:  1.36 (0.19), residues: 802
  sheet:  0.55 (0.55), residues: 80
  loop :  0.06 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.003   0.000   HIS A 153 
 PHE   0.016   0.001   PHE A 336 
 TYR   0.011   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A 915 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.7925 (mp0) cc_final: 0.7524 (mt-10)
REVERT: A   74 ASP cc_start: 0.7901 (t0) cc_final: 0.7144 (t0)
REVERT: A  126 MET cc_start: 0.7292 (mpp) cc_final: 0.6670 (ppp)
REVERT: A  186 MET cc_start: 0.6610 (tpp) cc_final: 0.6370 (ttm)
REVERT: A  345 VAL cc_start: 0.8666 (p) cc_final: 0.8419 (m)
REVERT: A  887 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7595 (mtt90)
REVERT: A  890 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7400 (mmtm)
REVERT: A  926 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7812 (tp)
REVERT: A 1018 ASP cc_start: 0.7260 (t70) cc_final: 0.7008 (t70)
REVERT: A 1107 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8127 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8231 (mp) cc_final: 0.7998 (mp)
REVERT: A 1155 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6391 (tt)
  outliers start: 11
  outliers final: 4
  residues processed: 95
  average time/residue: 0.2288
  time to fit residues: 31.2439
Evaluate side-chains
  85 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1155 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:   20.0000
   chunk 118 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0870
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
A 387 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.249779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.184523 restraints weight = 10113.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 1.95
r_work: 0.3529 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9936  Z= 0.185
  Angle     :  0.474   8.658  13463  Z= 0.248
  Chirality :  0.039   0.152   1561
  Planarity :  0.003   0.046   1673
  Dihedral  :  3.783  15.896   1314
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.39 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.40 (0.24), residues: 1212
  helix:  1.36 (0.19), residues: 802
  sheet:  0.65 (0.55), residues: 80
  loop :  0.13 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 733 
 HIS   0.005   0.001   HIS A 153 
 PHE   0.021   0.001   PHE A 389 
 TYR   0.012   0.001   TYR A 157 
 ARG   0.004   0.000   ARG A1220 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.7949 (mp0) cc_final: 0.7561 (mt-10)
REVERT: A   76 GLN cc_start: 0.8104 (pm20) cc_final: 0.7727 (pm20)
REVERT: A  126 MET cc_start: 0.7315 (mpp) cc_final: 0.6682 (ppp)
REVERT: A  345 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8417 (m)
REVERT: A  887 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7447 (mtt180)
REVERT: A  890 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7603 (mptt)
REVERT: A  926 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7743 (tp)
REVERT: A 1018 ASP cc_start: 0.7304 (t70) cc_final: 0.6999 (t0)
REVERT: A 1107 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8227 (mp) cc_final: 0.7974 (mp)
REVERT: A 1155 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6324 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 92
  average time/residue: 0.2155
  time to fit residues: 28.8008
Evaluate side-chains
  93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  840 PHE
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1155 LEU
Chi-restraints excluded: chain A residue 1187 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:   30.0000
   chunk 99 optimal weight:    9.9990
   chunk 112 optimal weight:    0.4980
   chunk 76 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 32 optimal weight:    0.5980
   chunk 56 optimal weight:    5.9990
   chunk 119 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.250012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.184636 restraints weight = 10143.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.90
r_work: 0.3544 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9936  Z= 0.179
  Angle     :  0.471   8.129  13463  Z= 0.246
  Chirality :  0.039   0.144   1561
  Planarity :  0.003   0.054   1673
  Dihedral  :  3.746  15.699   1314
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.58 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.54 (0.24), residues: 1212
  helix:  1.46 (0.19), residues: 802
  sheet:  0.66 (0.55), residues: 80
  loop :  0.20 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  64 
 HIS   0.004   0.001   HIS A 153 
 PHE   0.018   0.001   PHE A 336 
 TYR   0.011   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A1220 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.8188 (mp0) cc_final: 0.7724 (mt-10)
REVERT: A   76 GLN cc_start: 0.8127 (pm20) cc_final: 0.7658 (pm20)
REVERT: A  126 MET cc_start: 0.7466 (mpp) cc_final: 0.6691 (ppp)
REVERT: A  268 PHE cc_start: 0.7929 (m-10) cc_final: 0.7696 (m-10)
REVERT: A  345 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (m)
REVERT: A  763 TRP cc_start: 0.8719 (t60) cc_final: 0.8412 (t-100)
REVERT: A  887 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7542 (mtt180)
REVERT: A  890 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7693 (mptt)
REVERT: A  926 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7793 (tp)
REVERT: A 1018 ASP cc_start: 0.7654 (t70) cc_final: 0.7353 (t0)
REVERT: A 1107 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8006 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8082 (mp) cc_final: 0.7821 (mp)
REVERT: A 1155 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6324 (tt)
REVERT: A 1245 MET cc_start: 0.8654 (mtt) cc_final: 0.8194 (mtp)
  outliers start: 13
  outliers final: 8
  residues processed: 92
  average time/residue: 0.2128
  time to fit residues: 29.0466
Evaluate side-chains
  94 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  840 PHE
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1155 LEU
Chi-restraints excluded: chain A residue 1187 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    0.3980
   chunk 59 optimal weight:    0.1980
   chunk 56 optimal weight:    8.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.249840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.183830 restraints weight = 10067.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 1.93
r_work: 0.3538 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9936  Z= 0.178
  Angle     :  0.467   7.670  13463  Z= 0.244
  Chirality :  0.039   0.144   1561
  Planarity :  0.003   0.052   1673
  Dihedral  :  3.704  15.632   1314
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.86 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.59 (0.24), residues: 1212
  helix:  1.51 (0.19), residues: 798
  sheet:  0.74 (0.55), residues: 80
  loop :  0.21 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.005   0.001   HIS A 153 
 PHE   0.019   0.001   PHE A 389 
 TYR   0.012   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A1182 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.8017 (mp0) cc_final: 0.7719 (mt-10)
REVERT: A   76 GLN cc_start: 0.8142 (pm20) cc_final: 0.7800 (pm20)
REVERT: A  126 MET cc_start: 0.7392 (mpp) cc_final: 0.6768 (ppp)
REVERT: A  345 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8377 (m)
REVERT: A  763 TRP cc_start: 0.8624 (t60) cc_final: 0.8345 (t-100)
REVERT: A  805 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7784 (tt)
REVERT: A  887 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7401 (mtt90)
REVERT: A  890 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7623 (mptt)
REVERT: A  897 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.6318 (ttt-90)
REVERT: A  926 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7792 (tp)
REVERT: A 1107 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8268 (mp) cc_final: 0.8008 (mp)
REVERT: A 1155 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6535 (tt)
REVERT: A 1183 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8256 (mm-40)
REVERT: A 1245 MET cc_start: 0.8800 (mtt) cc_final: 0.8284 (mtp)
  outliers start: 12
  outliers final: 7
  residues processed: 92
  average time/residue: 0.2217
  time to fit residues: 29.8069
Evaluate side-chains
  93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  840 PHE
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1155 LEU
Chi-restraints excluded: chain A residue 1187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:   30.0000
   chunk 17 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0020
   overall best weight:    0.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.251118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.185845 restraints weight = 10067.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 1.91
r_work: 0.3589 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9936  Z= 0.157
  Angle     :  0.457   7.622  13463  Z= 0.239
  Chirality :  0.039   0.140   1561
  Planarity :  0.003   0.050   1673
  Dihedral  :  3.640  14.927   1314
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.24 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.76 (0.25), residues: 1212
  helix:  1.64 (0.19), residues: 797
  sheet:  0.82 (0.55), residues: 80
  loop :  0.27 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A 153 
 PHE   0.019   0.001   PHE A 389 
 TYR   0.011   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A1220 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 1.068 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.8192 (mp0) cc_final: 0.7803 (mt-10)
REVERT: A   74 ASP cc_start: 0.8363 (t0) cc_final: 0.8050 (t0)
REVERT: A  126 MET cc_start: 0.7523 (mpp) cc_final: 0.6761 (ppp)
REVERT: A  345 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (m)
REVERT: A  887 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7498 (mtt90)
REVERT: A  890 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7712 (mptt)
REVERT: A  897 ARG cc_start: 0.6766 (ttm-80) cc_final: 0.6410 (ttt-90)
REVERT: A  926 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7802 (tp)
REVERT: A 1107 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7984 (mt-10)
REVERT: A 1135 LEU cc_start: 0.8099 (mp) cc_final: 0.7855 (mp)
REVERT: A 1155 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6314 (tt)
REVERT: A 1183 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8160 (mm-40)
  outliers start: 11
  outliers final: 7
  residues processed: 90
  average time/residue: 0.2452
  time to fit residues: 31.5510
Evaluate side-chains
  90 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  840 PHE
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1155 LEU
Chi-restraints excluded: chain A residue 1187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 18 optimal weight:    0.1980
   chunk 60 optimal weight:    7.9990
   chunk 59 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.250656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.185287 restraints weight = 9927.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 1.93
r_work: 0.3579 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9936  Z= 0.164
  Angle     :  0.466   7.517  13463  Z= 0.243
  Chirality :  0.039   0.143   1561
  Planarity :  0.003   0.050   1673
  Dihedral  :  3.600  14.988   1314
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.05 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.85 (0.25), residues: 1212
  helix:  1.68 (0.19), residues: 797
  sheet:  0.92 (0.55), residues: 80
  loop :  0.35 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A 153 
 PHE   0.018   0.001   PHE A 389 
 TYR   0.012   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A1220 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5506.77 seconds
wall clock time: 98 minutes 30.45 seconds (5910.45 seconds total)