Starting phenix.real_space_refine
on Sat Aug 23 04:20:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wi2_37555/08_2025/8wi2_37555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wi2_37555/08_2025/8wi2_37555.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wi2_37555/08_2025/8wi2_37555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wi2_37555/08_2025/8wi2_37555.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wi2_37555/08_2025/8wi2_37555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wi2_37555/08_2025/8wi2_37555.map"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.035
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      57      5.16       5
     C    6131      2.51       5
     N    1621      2.21       5
     O    1728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9537
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1200, 9439
          Classifications: {'peptide': 1200}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1163}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 98
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 1.95, per 1000 atoms: 0.20
  Number of scatterers: 9537
  At special positions: 0
  Unit cell: (76.95, 113.715, 153.9, 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      57     16.00
     O    1728      8.00
     N    1621      7.00
     C    6131      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: 0.79
  Conformation dependent library (CDL) restraints added in 370.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2286

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 7 sheets defined
      69.6% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 112
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 129 through 133
      removed outlier: 3.725A  pdb=" N   VAL A 133 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 140
    Processing helix  chain 'A' and resid 141 through 161
    Processing helix  chain 'A' and resid 166 through 210
      removed outlier: 3.644A  pdb=" N   VAL A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   THR A 177 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ARG A 178 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 214 through 264
      removed outlier: 3.729A  pdb=" N   SER A 218 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU A 220 " --> pdb=" O   GLN A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 279
    Processing helix  chain 'A' and resid 282 through 298
    Processing helix  chain 'A' and resid 300 through 316
    Processing helix  chain 'A' and resid 318 through 324
      removed outlier: 4.174A  pdb=" N   GLY A 322 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 364
      Proline residue:  A 331  - end of helix
      removed outlier: 3.763A  pdb=" N   ALA A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   TYR A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
    Processing helix  chain 'A' and resid 373 through 402
      removed outlier: 3.937A  pdb=" N   PHE A 377 " --> pdb=" O   TRP A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 424
      removed outlier: 4.195A  pdb=" N   ILE A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 470
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 600 through 610
    Processing helix  chain 'A' and resid 638 through 645
      removed outlier: 3.708A  pdb=" N   ASN A 642 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU A 644 " --> pdb=" O   ARG A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 661
    Processing helix  chain 'A' and resid 663 through 670
      removed outlier: 3.535A  pdb=" N   LEU A 670 " --> pdb=" O   ASP A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 676
      removed outlier: 3.632A  pdb=" N   THR A 676 " --> pdb=" O   SER A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
      removed outlier: 3.688A  pdb=" N   ASP A 702 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 728
    Processing helix  chain 'A' and resid 744 through 748
      removed outlier: 3.731A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   VAL A 748 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 744 through 748'
    Processing helix  chain 'A' and resid 766 through 773
    Processing helix  chain 'A' and resid 775 through 786
      removed outlier: 3.758A  pdb=" N   THR A 779 " --> pdb=" O   GLY A 775 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN A 783 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A 784 " --> pdb=" O   ILE A 780 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU A 785 " --> pdb=" O   PHE A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 854
      removed outlier: 4.119A  pdb=" N   TYR A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 887
      removed outlier: 3.982A  pdb=" N   PHE A 859 " --> pdb=" O   GLY A 855 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY A 887 " --> pdb=" O   TRP A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 908
    Processing helix  chain 'A' and resid 910 through 956
    Processing helix  chain 'A' and resid 959 through 966
      removed outlier: 4.406A  pdb=" N   PHE A 963 " --> pdb=" O   PRO A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 1011
      removed outlier: 4.167A  pdb=" N   ILE A 971 " --> pdb=" O   PRO A 967 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ASP A 978 " --> pdb=" O   ARG A 974 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   MET A 979 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP A 980 " --> pdb=" O   SER A 976 " (cutoff:3.500A)
      Proline residue:  A 987  - end of helix
    Processing helix  chain 'A' and resid 1011 through 1060
      removed outlier: 3.800A  pdb=" N   LEU A1015 " --> pdb=" O   PHE A1011 " (cutoff:3.500A)
      Proline residue:  A1020  - end of helix
      Proline residue:  A1049  - end of helix
      removed outlier: 3.771A  pdb=" N   GLY A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1068
    Processing helix  chain 'A' and resid 1069 through 1120
      removed outlier: 3.549A  pdb=" N   PHE A1073 " --> pdb=" O   LYS A1069 " (cutoff:3.500A)
      Proline residue:  A1087  - end of helix
      removed outlier: 3.892A  pdb=" N   MET A1120 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1139
      removed outlier: 3.505A  pdb=" N   ALA A1129 " --> pdb=" O   PRO A1125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1169
    Processing helix  chain 'A' and resid 1234 through 1241
      removed outlier: 4.026A  pdb=" N   MET A1238 " --> pdb=" O   SER A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1261
      No H-bonds generated for 'chain 'A' and resid 1259 through 1261'
    Processing helix  chain 'A' and resid 1262 through 1268
    Processing helix  chain 'A' and resid 1284 through 1289
    Processing helix  chain 'A' and resid 1295 through 1307
    Processing helix  chain 'A' and resid 1308 through 1312
    Processing helix  chain 'A' and resid 1324 through 1328
      removed outlier: 3.721A  pdb=" N   ASP A1328 " --> pdb=" O   GLU A1325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1345
    Processing helix  chain 'A' and resid 1363 through 1376
      removed outlier: 3.585A  pdb=" N   PHE A1376 " --> pdb=" O   ILE A1372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1387 through 1392
      removed outlier: 3.518A  pdb=" N   VAL A1391 " --> pdb=" O   ARG A1387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1416
    Processing helix  chain 'A' and resid 1420 through 1424
    Processing helix  chain 'B' and resid 50 through 59
      removed outlier: 3.761A  pdb=" N   ALA B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG B  55 " --> pdb=" O   GLU B  51 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLU B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY B  58 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 576 through 585
      removed outlier: 6.902A  pdb=" N   LEU A 497 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   HIS A 579 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   ALA A 495 " --> pdb=" O   HIS A 579 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE A 581 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   LYS A 493 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LEU A 583 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   GLU A 491 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER A 618 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 626
      removed outlier: 5.823A  pdb=" N   ALA A 626 " --> pdb=" O   ILE A 707 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ASP A 709 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL A 740 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LEU A 708 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL A 591 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU A 590 " --> pdb=" O   GLU A 752 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ILE A 754 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLY A 592 " --> pdb=" O   ILE A 754 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   MET A 756 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   CYS A 594 " --> pdb=" O   MET A 756 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   VAL A 753 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   ARG A 764 " --> pdb=" O   VAL A 753 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   PHE A 755 " --> pdb=" O   THR A 762 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   THR A 762 " --> pdb=" O   PHE A 755 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A 757 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 892 through 894
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1217
      removed outlier: 3.504A  pdb=" N   VAL A1193 " --> pdb=" O   ILE A1217 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1200 through 1201
      removed outlier: 3.534A  pdb=" N   MET A1200 " --> pdb=" O   LEU A1210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1270 through 1273
      removed outlier: 3.699A  pdb=" N   SER A1271 " --> pdb=" O   ILE A1350 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A1352 " --> pdb=" O   SER A1271 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A1351 " --> pdb=" O   THR A1380 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A1382 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ILE A1223 " --> pdb=" O   THR A1383 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LYS A1222 " --> pdb=" O   ARG A1396 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   MET A1398 " --> pdb=" O   LYS A1222 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   GLY A1224 " --> pdb=" O   MET A1398 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   LEU A1400 " --> pdb=" O   GLY A1224 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL A1226 " --> pdb=" O   LEU A1400 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1282 through 1283

    610 hydrogen bonds defined for protein.
    1788 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: 1.11

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3073
        1.35 -     1.46: 2216
        1.46 -     1.58: 4334
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 9719
  Sorted by residual:
  bond pdb=" CA  THR A 450 "
       pdb=" C   THR A 450 "
    ideal  model  delta    sigma   weight residual
    1.522  1.542 -0.021 1.26e-02 6.30e+03 2.65e+00
  bond pdb=" CG  MET A 370 "
       pdb=" SD  MET A 370 "
    ideal  model  delta    sigma   weight residual
    1.803  1.774  0.029 2.50e-02 1.60e+03 1.37e+00
  bond pdb=" CA  SER A1048 "
       pdb=" C   SER A1048 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 1.23e-02 6.61e+03 1.10e+00
  bond pdb=" CA  ILE A1384 "
       pdb=" CB  ILE A1384 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.36e-02 5.41e+03 1.04e+00
  bond pdb=" CB  ASP A 980 "
       pdb=" CG  ASP A 980 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.62e-01
  ... (remaining 9714 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 12841
        1.73 -     3.46: 233
        3.46 -     5.19: 48
        5.19 -     6.92: 21
        6.92 -     8.65: 11
  Bond angle restraints: 13154
  Sorted by residual:
  angle pdb=" N   MET A 443 "
        pdb=" CA  MET A 443 "
        pdb=" CB  MET A 443 "
      ideal   model   delta    sigma   weight residual
     110.28  116.35   -6.07 1.55e+00 4.16e-01 1.54e+01
  angle pdb=" C   LYS A 369 "
        pdb=" N   MET A 370 "
        pdb=" CA  MET A 370 "
      ideal   model   delta    sigma   weight residual
     121.94  114.99    6.95 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" N   THR A 450 "
        pdb=" CA  THR A 450 "
        pdb=" C   THR A 450 "
      ideal   model   delta    sigma   weight residual
     113.16  117.62   -4.46 1.42e+00 4.96e-01 9.86e+00
  angle pdb=" C   SER A 442 "
        pdb=" N   MET A 443 "
        pdb=" CA  MET A 443 "
      ideal   model   delta    sigma   weight residual
     120.31  115.78    4.53 1.52e+00 4.33e-01 8.87e+00
  angle pdb=" N   GLY A1070 "
        pdb=" CA  GLY A1070 "
        pdb=" C   GLY A1070 "
      ideal   model   delta    sigma   weight residual
     112.73  115.90   -3.17 1.20e+00 6.94e-01 6.97e+00
  ... (remaining 13149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4936
       17.82 -    35.64: 673
       35.64 -    53.45: 188
       53.45 -    71.27: 22
       71.27 -    89.09: 17
  Dihedral angle restraints: 5836
    sinusoidal: 2312
      harmonic: 3524
  Sorted by residual:
  dihedral pdb=" CA  THR A 450 "
           pdb=" C   THR A 450 "
           pdb=" N   PRO A 451 "
           pdb=" CA  PRO A 451 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.58  -18.42     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ASP A1378 "
           pdb=" CB  ASP A1378 "
           pdb=" CG  ASP A1378 "
           pdb=" OD1 ASP A1378 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.83   59.83     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  ASP A 776 "
           pdb=" CB  ASP A 776 "
           pdb=" CG  ASP A 776 "
           pdb=" OD1 ASP A 776 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.88   56.88     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 5833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1221
       0.046 -    0.092: 258
       0.092 -    0.138: 60
       0.138 -    0.184: 4
       0.184 -    0.230: 1
  Chirality restraints: 1544
  Sorted by residual:
  chirality pdb=" CB  ILE A 180 "
            pdb=" CA  ILE A 180 "
            pdb=" CG1 ILE A 180 "
            pdb=" CG2 ILE A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  THR A 450 "
            pdb=" N   THR A 450 "
            pdb=" C   THR A 450 "
            pdb=" CB  THR A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" CA  MET A 443 "
            pdb=" N   MET A 443 "
            pdb=" C   MET A 443 "
            pdb=" CB  MET A 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.65e-01
  ... (remaining 1541 not shown)

  Planarity restraints: 1645
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 316 "    0.039 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO A 317 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 330 "    0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO A 331 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 982 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   VAL A 982 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A 982 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 983 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1642 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 160
        2.66 -     3.22: 9490
        3.22 -     3.78: 15817
        3.78 -     4.34: 18947
        4.34 -     4.90: 31029
  Nonbonded interactions: 75443
  Sorted by model distance:
  nonbonded pdb=" O   THR A 450 "
            pdb=" OG  SER A 453 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OG1 THR A 496 "
            pdb=" OE1 GLU A 616 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   ASN A 359 "
            pdb=" OG1 THR A 363 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 186 "
            pdb=" OG1 THR A 189 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER A 137 "
            pdb=" OE1 GLU A 140 "
     model   vdw
     2.258 3.040
  ... (remaining 75438 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  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:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.600
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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      :  0.003   0.033   9719  Z= 0.141
  Angle     :  0.660   8.654  13154  Z= 0.344
  Chirality :  0.040   0.230   1544
  Planarity :  0.004   0.060   1645
  Dihedral  : 17.703  89.089   3550
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 32.38 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.25), residues: 1202
  helix:  2.13 (0.19), residues: 753
  sheet:  2.30 (0.71), residues: 64
  loop : -0.07 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.016   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A1014 
 TRP   0.021   0.001   TRP A 240 
 HIS   0.002   0.001   HIS A1165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9719)
  covalent geometry    : angle       0.66034 (13154)
  hydrogen bonds       : bond        0.12293 (  610)
  hydrogen bonds       : angle       5.20896 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  886 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8779 (tp40)
REVERT: A 1238 MET cc_start: 0.9115 (mpp) cc_final: 0.8861 (mpp)
  outliers start: 7
  outliers final: 3
  residues processed: 110
  average time/residue: 0.0636
  time to fit residues: 10.9564
Evaluate side-chains
  105 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 575 GLN
A 611 GLN
A 721 ASN
A 908 ASN
A 996 ASN
A1121 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.090650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.076612 restraints weight = 50761.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.078475 restraints weight = 27371.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.079755 restraints weight = 17474.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.080653 restraints weight = 12638.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.080973 restraints weight = 9937.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9719  Z= 0.150
  Angle     :  0.589   7.349  13154  Z= 0.306
  Chirality :  0.040   0.184   1544
  Planarity :  0.004   0.057   1645
  Dihedral  :  3.781  15.707   1305
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.34 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.25), residues: 1202
  helix:  2.05 (0.19), residues: 758
  sheet:  1.92 (0.65), residues: 74
  loop : -0.21 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1148 
 TYR   0.017   0.001   TYR A 342 
 PHE   0.022   0.002   PHE A1145 
 TRP   0.038   0.002   TRP A 114 
 HIS   0.003   0.001   HIS A1165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9719)
  covalent geometry    : angle       0.58909 (13154)
  hydrogen bonds       : bond        0.06120 (  610)
  hydrogen bonds       : angle       4.65921 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9295 (mmm) cc_final: 0.8968 (tpp)
REVERT: A  771 MET cc_start: 0.5392 (mpp) cc_final: 0.5008 (mpp)
REVERT: A 1077 TYR cc_start: 0.9147 (t80) cc_final: 0.8852 (t80)
REVERT: A 1095 MET cc_start: 0.8034 (ttm) cc_final: 0.7340 (ttm)
REVERT: A 1103 ASP cc_start: 0.7917 (t0) cc_final: 0.7676 (t0)
REVERT: A 1238 MET cc_start: 0.8497 (mpp) cc_final: 0.8167 (mpp)
REVERT: A 1389 HIS cc_start: 0.8325 (m90) cc_final: 0.7967 (m90)
  outliers start: 2
  outliers final: 1
  residues processed: 154
  average time/residue: 0.0748
  time to fit residues: 16.8401
Evaluate side-chains
  101 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 60 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 782 ASN
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.084779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.069572 restraints weight = 50934.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071331 restraints weight = 28416.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.072522 restraints weight = 18659.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.073214 restraints weight = 13879.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.073830 restraints weight = 11375.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9719  Z= 0.244
  Angle     :  0.671   8.565  13154  Z= 0.358
  Chirality :  0.042   0.188   1544
  Planarity :  0.005   0.059   1645
  Dihedral  :  4.056  17.441   1305
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.11 %
    Favored  : 93.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.24), residues: 1202
  helix:  1.71 (0.18), residues: 754
  sheet:  1.72 (0.63), residues: 72
  loop : -0.30 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  55 
 TYR   0.029   0.002   TYR A 918 
 PHE   0.021   0.002   PHE A 434 
 TRP   0.014   0.002   TRP A 499 
 HIS   0.006   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 9719)
  covalent geometry    : angle       0.67053 (13154)
  hydrogen bonds       : bond        0.07181 (  610)
  hydrogen bonds       : angle       4.95719 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9309 (mmm) cc_final: 0.9085 (tpp)
REVERT: A  422 MET cc_start: 0.8613 (tpt) cc_final: 0.8382 (tpp)
REVERT: A  771 MET cc_start: 0.5489 (mpp) cc_final: 0.5189 (mpp)
REVERT: A  905 MET cc_start: 0.8032 (mmm) cc_final: 0.7703 (mmm)
REVERT: A 1103 ASP cc_start: 0.8105 (t0) cc_final: 0.7896 (t0)
REVERT: A 1238 MET cc_start: 0.8632 (mpp) cc_final: 0.8311 (mpp)
REVERT: A 1308 MET cc_start: 0.8140 (tpp) cc_final: 0.7695 (tpp)
REVERT: A 1389 HIS cc_start: 0.8269 (m90) cc_final: 0.7954 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0713
  time to fit residues: 12.9929
Evaluate side-chains
  88 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 7 optimal weight:    0.4980
   chunk 108 optimal weight:    0.1980
   chunk 23 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 973 ASN
A 996 ASN
** A1336 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 = 0.3843 r_free = 0.3843 target = 0.085744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.071414 restraints weight = 48111.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.073285 restraints weight = 25534.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.074523 restraints weight = 16126.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.075384 restraints weight = 11524.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.075829 restraints weight = 9076.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9719  Z= 0.139
  Angle     :  0.565   7.686  13154  Z= 0.292
  Chirality :  0.040   0.176   1544
  Planarity :  0.004   0.056   1645
  Dihedral  :  3.838  16.387   1305
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.25), residues: 1202
  helix:  1.92 (0.18), residues: 758
  sheet:  1.63 (0.64), residues: 72
  loop : -0.31 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  55 
 TYR   0.022   0.001   TYR A 918 
 PHE   0.017   0.001   PHE A1050 
 TRP   0.014   0.001   TRP A 240 
 HIS   0.002   0.001   HIS A 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9719)
  covalent geometry    : angle       0.56482 (13154)
  hydrogen bonds       : bond        0.06331 (  610)
  hydrogen bonds       : angle       4.45729 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9360 (mmm) cc_final: 0.9119 (tpp)
REVERT: A  287 MET cc_start: 0.9084 (mmp) cc_final: 0.8734 (mmt)
REVERT: A  310 TYR cc_start: 0.8522 (t80) cc_final: 0.8187 (t80)
REVERT: A  612 MET cc_start: 0.0777 (tpt) cc_final: 0.0060 (tpt)
REVERT: A  771 MET cc_start: 0.5154 (mpp) cc_final: 0.4844 (mpp)
REVERT: A  911 MET cc_start: 0.7777 (ppp) cc_final: 0.7356 (ppp)
REVERT: A 1103 ASP cc_start: 0.8057 (t0) cc_final: 0.7805 (t0)
REVERT: A 1238 MET cc_start: 0.8677 (mpp) cc_final: 0.8347 (mpp)
REVERT: A 1389 HIS cc_start: 0.8290 (m90) cc_final: 0.7965 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0584
  time to fit residues: 11.6899
Evaluate side-chains
  95 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0970
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.087052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.072564 restraints weight = 49131.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.074387 restraints weight = 26857.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.075602 restraints weight = 17202.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.076461 restraints weight = 12517.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.076756 restraints weight = 9975.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9719  Z= 0.134
  Angle     :  0.564   7.236  13154  Z= 0.290
  Chirality :  0.039   0.180   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.814  15.609   1305
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.25), residues: 1202
  helix:  1.98 (0.18), residues: 758
  sheet:  1.56 (0.64), residues: 72
  loop : -0.25 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  55 
 TYR   0.016   0.001   TYR A 342 
 PHE   0.019   0.001   PHE A 335 
 TRP   0.012   0.001   TRP A 240 
 HIS   0.002   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9719)
  covalent geometry    : angle       0.56446 (13154)
  hydrogen bonds       : bond        0.06071 (  610)
  hydrogen bonds       : angle       4.41614 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9372 (mmm) cc_final: 0.9146 (tpp)
REVERT: A  310 TYR cc_start: 0.8531 (t80) cc_final: 0.8311 (t80)
REVERT: A  612 MET cc_start: 0.0571 (tpt) cc_final: -0.0284 (tpt)
REVERT: A  771 MET cc_start: 0.4747 (mpp) cc_final: 0.4455 (mpp)
REVERT: A  911 MET cc_start: 0.7589 (ppp) cc_final: 0.7327 (ppp)
REVERT: A  960 MET cc_start: 0.7711 (mtm) cc_final: 0.7386 (mtm)
REVERT: A 1103 ASP cc_start: 0.8064 (t0) cc_final: 0.7832 (t0)
REVERT: A 1238 MET cc_start: 0.8676 (mpp) cc_final: 0.8334 (mpp)
REVERT: A 1308 MET cc_start: 0.8135 (tpp) cc_final: 0.7740 (tpp)
REVERT: A 1389 HIS cc_start: 0.8327 (m90) cc_final: 0.8009 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0805
  time to fit residues: 15.5979
Evaluate side-chains
  102 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 10 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 102 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 GLN
A 996 ASN
A1047 GLN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.085110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.070659 restraints weight = 48209.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.072454 restraints weight = 26037.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.073678 restraints weight = 16741.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.074542 restraints weight = 12148.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.075015 restraints weight = 9591.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9719  Z= 0.158
  Angle     :  0.580   8.206  13154  Z= 0.299
  Chirality :  0.040   0.177   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.825  16.167   1305
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.48 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.24), residues: 1202
  helix:  1.94 (0.18), residues: 759
  sheet:  1.39 (0.63), residues: 72
  loop : -0.17 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  55 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.019   0.002   PHE A 988 
 TRP   0.022   0.001   TRP A 883 
 HIS   0.003   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9719)
  covalent geometry    : angle       0.57966 (13154)
  hydrogen bonds       : bond        0.06272 (  610)
  hydrogen bonds       : angle       4.48160 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9405 (mmm) cc_final: 0.9173 (tpp)
REVERT: A  771 MET cc_start: 0.4946 (mpp) cc_final: 0.4620 (mpp)
REVERT: A  911 MET cc_start: 0.7712 (ppp) cc_final: 0.7496 (ppp)
REVERT: A 1103 ASP cc_start: 0.8119 (t0) cc_final: 0.7841 (t0)
REVERT: A 1139 LEU cc_start: 0.9026 (tp) cc_final: 0.8795 (tt)
REVERT: A 1238 MET cc_start: 0.8683 (mpp) cc_final: 0.8422 (mpp)
REVERT: A 1308 MET cc_start: 0.8101 (tpp) cc_final: 0.7764 (tpp)
REVERT: A 1389 HIS cc_start: 0.8347 (m90) cc_final: 0.8022 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0705
  time to fit residues: 14.2935
Evaluate side-chains
  98 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 103 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 87 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
** A1336 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 = 0.3831 r_free = 0.3831 target = 0.085515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.071227 restraints weight = 48236.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.073038 restraints weight = 25884.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.074280 restraints weight = 16515.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.075129 restraints weight = 11840.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.075576 restraints weight = 9336.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9719  Z= 0.147
  Angle     :  0.586   7.101  13154  Z= 0.301
  Chirality :  0.040   0.180   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.865  16.894   1305
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.24), residues: 1202
  helix:  2.00 (0.18), residues: 758
  sheet:  1.31 (0.63), residues: 72
  loop : -0.19 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  55 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.017   0.001   PHE A 335 
 TRP   0.022   0.001   TRP A 883 
 HIS   0.003   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9719)
  covalent geometry    : angle       0.58557 (13154)
  hydrogen bonds       : bond        0.06208 (  610)
  hydrogen bonds       : angle       4.45855 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9406 (mmm) cc_final: 0.9184 (tpp)
REVERT: A  310 TYR cc_start: 0.8534 (t80) cc_final: 0.8100 (t80)
REVERT: A  771 MET cc_start: 0.4908 (mpp) cc_final: 0.4535 (mpp)
REVERT: A 1103 ASP cc_start: 0.8113 (t0) cc_final: 0.7848 (t0)
REVERT: A 1139 LEU cc_start: 0.9054 (tp) cc_final: 0.8795 (tt)
REVERT: A 1308 MET cc_start: 0.8093 (tpp) cc_final: 0.7799 (tpp)
REVERT: A 1389 HIS cc_start: 0.8359 (m90) cc_final: 0.8048 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0668
  time to fit residues: 12.7887
Evaluate side-chains
  95 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 96 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 110 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0980
   chunk 74 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
A1085 GLN
A1336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.087661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.073497 restraints weight = 49247.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.075320 restraints weight = 26771.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.076548 restraints weight = 17174.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.077260 restraints weight = 12492.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.077878 restraints weight = 10107.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9719  Z= 0.127
  Angle     :  0.594   8.351  13154  Z= 0.294
  Chirality :  0.040   0.180   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.767  15.932   1305
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.25), residues: 1202
  helix:  2.09 (0.19), residues: 757
  sheet:  1.15 (0.60), residues: 77
  loop : -0.19 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  55 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.021   0.001   PHE A 988 
 TRP   0.016   0.001   TRP A 883 
 HIS   0.002   0.000   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9719)
  covalent geometry    : angle       0.59408 (13154)
  hydrogen bonds       : bond        0.05687 (  610)
  hydrogen bonds       : angle       4.30414 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  771 MET cc_start: 0.4719 (mpp) cc_final: 0.4309 (mpp)
REVERT: A 1103 ASP cc_start: 0.7993 (t0) cc_final: 0.7778 (t0)
REVERT: A 1139 LEU cc_start: 0.9041 (tp) cc_final: 0.8814 (tt)
REVERT: A 1324 MET cc_start: 0.7965 (pmm) cc_final: 0.7733 (pmm)
REVERT: A 1389 HIS cc_start: 0.8306 (m90) cc_final: 0.8001 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0741
  time to fit residues: 14.6470
Evaluate side-chains
  97 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 117 optimal weight:    0.0570
   chunk 67 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 115 optimal weight:   30.0000
   chunk 3 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.9302

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1386 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.085854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071445 restraints weight = 49124.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.073196 restraints weight = 27137.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.074387 restraints weight = 17608.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.075177 restraints weight = 12843.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.075608 restraints weight = 10315.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9719  Z= 0.151
  Angle     :  0.606   7.224  13154  Z= 0.306
  Chirality :  0.040   0.175   1544
  Planarity :  0.004   0.053   1645
  Dihedral  :  3.805  16.284   1305
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.24), residues: 1202
  helix:  2.02 (0.18), residues: 762
  sheet:  1.19 (0.62), residues: 72
  loop : -0.18 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  55 
 TYR   0.014   0.001   TYR A 342 
 PHE   0.015   0.002   PHE A 335 
 TRP   0.011   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9719)
  covalent geometry    : angle       0.60609 (13154)
  hydrogen bonds       : bond        0.06034 (  610)
  hydrogen bonds       : angle       4.40003 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A 1095 MET cc_start: 0.7798 (ttm) cc_final: 0.7583 (ttm)
REVERT: A 1103 ASP cc_start: 0.8102 (t0) cc_final: 0.7844 (t0)
REVERT: A 1139 LEU cc_start: 0.9012 (tp) cc_final: 0.8786 (tt)
REVERT: A 1389 HIS cc_start: 0.8434 (m90) cc_final: 0.8136 (m90)
REVERT: B   59 LEU cc_start: 0.8249 (mm) cc_final: 0.7617 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0658
  time to fit residues: 13.2863
Evaluate side-chains
  97 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   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 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.085884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.071563 restraints weight = 48880.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.073317 restraints weight = 26988.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.074544 restraints weight = 17553.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.075365 restraints weight = 12787.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.075786 restraints weight = 10236.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9719  Z= 0.141
  Angle     :  0.606   7.807  13154  Z= 0.304
  Chirality :  0.040   0.172   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.812  16.176   1305
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.24), residues: 1202
  helix:  2.01 (0.18), residues: 762
  sheet:  1.23 (0.62), residues: 72
  loop : -0.18 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  55 
 TYR   0.043   0.001   TYR A 918 
 PHE   0.014   0.001   PHE A 418 
 TRP   0.026   0.002   TRP A 883 
 HIS   0.003   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9719)
  covalent geometry    : angle       0.60618 (13154)
  hydrogen bonds       : bond        0.06014 (  610)
  hydrogen bonds       : angle       4.38614 ( 1788)

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  708 LEU cc_start: 0.8452 (tt) cc_final: 0.7203 (mp)
REVERT: A  905 MET cc_start: 0.8132 (mmm) cc_final: 0.7571 (mmm)
REVERT: A 1095 MET cc_start: 0.7772 (ttm) cc_final: 0.7571 (ttm)
REVERT: A 1103 ASP cc_start: 0.8107 (t0) cc_final: 0.7873 (t0)
REVERT: A 1139 LEU cc_start: 0.9025 (tp) cc_final: 0.8801 (tt)
REVERT: A 1389 HIS cc_start: 0.8397 (m90) cc_final: 0.8096 (m90)
REVERT: B   59 LEU cc_start: 0.8212 (mm) cc_final: 0.7516 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0626
  time to fit residues: 12.2680
Evaluate side-chains
  97 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0970
   chunk 83 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.087320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.073353 restraints weight = 48788.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.075133 restraints weight = 26933.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.076330 restraints weight = 17429.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.077167 restraints weight = 12681.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.077667 restraints weight = 10067.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9719  Z= 0.128
  Angle     :  0.614   8.659  13154  Z= 0.301
  Chirality :  0.040   0.171   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.779  15.685   1305
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.25), residues: 1202
  helix:  2.05 (0.18), residues: 763
  sheet:  1.06 (0.59), residues: 77
  loop : -0.13 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  55 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.023   0.001   PHE A 988 
 TRP   0.017   0.001   TRP A 114 
 HIS   0.003   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9719)
  covalent geometry    : angle       0.61388 (13154)
  hydrogen bonds       : bond        0.05608 (  610)
  hydrogen bonds       : angle       4.27840 ( 1788)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1378.07 seconds
wall clock time: 24 minutes 39.54 seconds (1479.54 seconds total)