Starting phenix.real_space_refine
on Wed Jan 15 15:42:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f42_50181/01_2025/9f42_50181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f42_50181/01_2025/9f42_50181.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f42_50181/01_2025/9f42_50181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f42_50181/01_2025/9f42_50181.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f42_50181/01_2025/9f42_50181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f42_50181/01_2025/9f42_50181.cif"
  }
  resolution = 3.27
  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=   0.037
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    5413      2.51       5
     N    1462      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8465
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "E"
      Number of atoms: 8385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1052, 8385
          Classifications: {'peptide': 1052}
          Link IDs: {'PTRANS': 56, 'TRANS': 995}
          Chain breaks: 5
    Chain: "G"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 80
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
  Time building chain proxies: 7.35, per 1000 atoms: 0.87
  Number of scatterers: 8465
  At special positions: 0
  Unit cell: (103.49, 144.1, 82.53, 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    1533      8.00
     N    1462      7.00
     C    5413      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: 2.33
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      47.7% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'E' and resid 19 through 25
      removed outlier: 4.112A  pdb=" N   ASP E  23 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 37
    Processing helix  chain 'E' and resid 89 through 93
    Processing helix  chain 'E' and resid 94 through 112
    Processing helix  chain 'E' and resid 126 through 141
    Processing helix  chain 'E' and resid 179 through 186
    Processing helix  chain 'E' and resid 198 through 219
      removed outlier: 3.581A  pdb=" N   ILE E 202 " --> pdb=" O   ASN E 198 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU E 218 " --> pdb=" O   GLU E 214 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   VAL E 219 " --> pdb=" O   GLN E 215 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 262 through 269
    Processing helix  chain 'E' and resid 269 through 279
    Processing helix  chain 'E' and resid 280 through 287
      removed outlier: 6.452A  pdb=" N   CYS E 283 " --> pdb=" O   MET E 280 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 291 through 297
    Processing helix  chain 'E' and resid 307 through 328
    Processing helix  chain 'E' and resid 329 through 338
      removed outlier: 3.649A  pdb=" N   ARG E 338 " --> pdb=" O   GLN E 334 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 359
      removed outlier: 3.868A  pdb=" N   LEU E 352 " --> pdb=" O   ARG E 348 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   SER E 359 " --> pdb=" O   ARG E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 377 through 392
      removed outlier: 3.676A  pdb=" N   ALA E 381 " --> pdb=" O   ALA E 377 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   GLN E 392 " --> pdb=" O   ILE E 388 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 392 through 398
    Processing helix  chain 'E' and resid 407 through 422
      removed outlier: 3.887A  pdb=" N   MET E 422 " --> pdb=" O   VAL E 418 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 432 through 442
      removed outlier: 3.754A  pdb=" N   LEU E 441 " --> pdb=" O   LEU E 437 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   SER E 442 " --> pdb=" O   GLN E 438 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 445 through 458
    Processing helix  chain 'E' and resid 460 through 471
    Processing helix  chain 'E' and resid 472 through 479
    Processing helix  chain 'E' and resid 480 through 482
      No H-bonds generated for 'chain 'E' and resid 480 through 482'
    Processing helix  chain 'E' and resid 486 through 502
      removed outlier: 4.809A  pdb=" N   LEU E 490 " --> pdb=" O   GLU E 486 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 504 through 512
      removed outlier: 4.564A  pdb=" N   ASP E 508 " --> pdb=" O   SER E 504 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 513 through 523
      removed outlier: 4.038A  pdb=" N   TYR E 517 " --> pdb=" O   ASN E 513 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 528 through 543
    Processing helix  chain 'E' and resid 546 through 556
    Processing helix  chain 'E' and resid 557 through 565
    Processing helix  chain 'E' and resid 570 through 585
      removed outlier: 3.538A  pdb=" N   TRP E 585 " --> pdb=" O   LEU E 581 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 588 through 598
    Processing helix  chain 'E' and resid 599 through 605
    Processing helix  chain 'E' and resid 606 through 610
    Processing helix  chain 'E' and resid 612 through 628
    Processing helix  chain 'E' and resid 634 through 649
    Processing helix  chain 'E' and resid 656 through 674
    Processing helix  chain 'E' and resid 674 through 685
      removed outlier: 3.758A  pdb=" N   PHE E 685 " --> pdb=" O   VAL E 681 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 807 through 820
    Processing helix  chain 'E' and resid 823 through 839
      removed outlier: 3.522A  pdb=" N   ILE E 837 " --> pdb=" O   VAL E 833 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   TYR E 839 " --> pdb=" O   ASN E 835 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 950 through 954
    Processing helix  chain 'E' and resid 958 through 965
    Processing helix  chain 'E' and resid 966 through 968
      No H-bonds generated for 'chain 'E' and resid 966 through 968'
    Processing helix  chain 'E' and resid 982 through 1008
    Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 123
      removed outlier: 7.548A  pdb=" N   VAL E  58 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   LYS E 120 " --> pdb=" O   VAL E  58 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL E  60 " --> pdb=" O   LYS E 120 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   SER E 122 " --> pdb=" O   VAL E  60 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LEU E  62 " --> pdb=" O   SER E 122 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ARG E 145 " --> pdb=" O   THR E  57 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   SER E  59 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   VAL E 146 " --> pdb=" O   ILE E 191 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   VAL E 193 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   PHE E 148 " --> pdb=" O   VAL E 193 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   ASP E 195 " --> pdb=" O   PHE E 148 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   TYR E 150 " --> pdb=" O   ASP E 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 163 through 167
    Processing sheet with id=AA3, first strand: chain 'E' and resid 1015 through 1016
      removed outlier: 3.929A  pdb=" N   ASP E1015 " --> pdb=" O   SER E1329 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER E1329 " --> pdb=" O   ASP E1015 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   CYS E1306 " --> pdb=" O   GLY E1319 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 1028 through 1031
      removed outlier: 3.626A  pdb=" N   VAL E1028 " --> pdb=" O   ALA E1041 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ILE E1046 " --> pdb=" O   TYR E1059 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   TYR E1059 " --> pdb=" O   ILE E1046 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   PHE E1048 " --> pdb=" O   LEU E1057 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 1070 through 1076
      removed outlier: 4.091A  pdb=" N   ALA E1092 " --> pdb=" O   THR E1088 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ILE E1093 " --> pdb=" O   ALA E1111 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ALA E1111 " --> pdb=" O   ILE E1093 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL E1095 " --> pdb=" O   VAL E1109 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 1127 through 1131
      removed outlier: 5.019A  pdb=" N   GLY E1142 " --> pdb=" O   ILE E1146 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ILE E1146 " --> pdb=" O   GLY E1142 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   VAL E1147 " --> pdb=" O   ASP E1160 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ASP E1160 " --> pdb=" O   VAL E1147 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE E1149 " --> pdb=" O   VAL E1158 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET E1156 " --> pdb=" O   ASP E1151 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 1169 through 1173
      removed outlier: 6.846A  pdb=" N   ILE E1190 " --> pdb=" O   THR E1206 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   THR E1206 " --> pdb=" O   ILE E1190 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   VAL E1192 " --> pdb=" O   VAL E1204 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 1214 through 1218
      removed outlier: 7.124A  pdb=" N   VAL E1230 " --> pdb=" O   VAL E1215 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA E1217 " --> pdb=" O   VAL E1228 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   VAL E1228 " --> pdb=" O   ALA E1217 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   SER E1231 " --> pdb=" O   ASP E1235 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ASP E1235 " --> pdb=" O   SER E1231 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN E1248 " --> pdb=" O   ILE E1238 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   ASP E1240 " --> pdb=" O   SER E1246 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   SER E1246 " --> pdb=" O   ASP E1240 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 1259 through 1260
      removed outlier: 3.721A  pdb=" N   ASN E1288 " --> pdb=" O   ILE E1279 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1158 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: 3.36

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2763
        1.34 -     1.46: 1717
        1.46 -     1.58: 4101
        1.58 -     1.69: 0
        1.69 -     1.81: 85
  Bond restraints: 8666
  Sorted by residual:
  bond pdb=" C   SER E 188 "
       pdb=" N   PRO E 189 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.57e-01
  bond pdb=" CA  ILE E1304 "
       pdb=" CB  ILE E1304 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 7.33e-01
  bond pdb=" C   PHE G 401 "
       pdb=" N   PHE G 402 "
    ideal  model  delta    sigma   weight residual
    1.333  1.344 -0.011 1.30e-02 5.92e+03 7.18e-01
  bond pdb=" N   CYS E  81 "
       pdb=" CA  CYS E  81 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.75e-01
  bond pdb=" CG1 ILE E 319 "
       pdb=" CD1 ILE E 319 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.25e-01
  ... (remaining 8661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 11628
        1.55 -     3.11: 125
        3.11 -     4.66: 24
        4.66 -     6.22: 9
        6.22 -     7.77: 1
  Bond angle restraints: 11787
  Sorted by residual:
  angle pdb=" C   PRO E  80 "
        pdb=" N   CYS E  81 "
        pdb=" CA  CYS E  81 "
      ideal   model   delta    sigma   weight residual
     121.54  126.79   -5.25 1.91e+00 2.74e-01 7.57e+00
  angle pdb=" CA  LEU E 390 "
        pdb=" CB  LEU E 390 "
        pdb=" CG  LEU E 390 "
      ideal   model   delta    sigma   weight residual
     116.30  124.07   -7.77 3.50e+00 8.16e-02 4.93e+00
  angle pdb=" C   CYS E  81 "
        pdb=" CA  CYS E  81 "
        pdb=" CB  CYS E  81 "
      ideal   model   delta    sigma   weight residual
     110.42  114.56   -4.14 1.99e+00 2.53e-01 4.34e+00
  angle pdb=" CA  LEU E1013 "
        pdb=" CB  LEU E1013 "
        pdb=" CG  LEU E1013 "
      ideal   model   delta    sigma   weight residual
     116.30  122.29   -5.99 3.50e+00 8.16e-02 2.93e+00
  angle pdb=" CA  TRP E 576 "
        pdb=" CB  TRP E 576 "
        pdb=" CG  TRP E 576 "
      ideal   model   delta    sigma   weight residual
     113.60  110.41    3.19 1.90e+00 2.77e-01 2.82e+00
  ... (remaining 11782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 4815
       16.78 -    33.55: 290
       33.55 -    50.33: 76
       50.33 -    67.10: 17
       67.10 -    83.88: 7
  Dihedral angle restraints: 5205
    sinusoidal: 2092
      harmonic: 3113
  Sorted by residual:
  dihedral pdb=" CA  PHE E1060 "
           pdb=" C   PHE E1060 "
           pdb=" N   HIS E1061 "
           pdb=" CA  HIS E1061 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.29   18.71     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ASN E1022 "
           pdb=" CB  ASN E1022 "
           pdb=" CG  ASN E1022 "
           pdb=" OD1 ASN E1022 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -155.06   65.06     2      2.00e+01 2.50e-03 9.87e+00
  dihedral pdb=" CB  GLU E 675 "
           pdb=" CG  GLU E 675 "
           pdb=" CD  GLU E 675 "
           pdb=" OE1 GLU E 675 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.88   83.88     1      3.00e+01 1.11e-03 9.53e+00
  ... (remaining 5202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 763
       0.026 -    0.052: 340
       0.052 -    0.077: 125
       0.077 -    0.103: 61
       0.103 -    0.129: 43
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CA  ILE E1279 "
            pdb=" N   ILE E1279 "
            pdb=" C   ILE E1279 "
            pdb=" CB  ILE E1279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ILE E 974 "
            pdb=" N   ILE E 974 "
            pdb=" C   ILE E 974 "
            pdb=" CB  ILE E 974 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  ILE E1190 "
            pdb=" N   ILE E1190 "
            pdb=" C   ILE E1190 "
            pdb=" CB  ILE E1190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1329 not shown)

  Planarity restraints: 1503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 298 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO E 299 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO E 299 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 299 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP E1313 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO E1314 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO E1314 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E1314 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E1161 "   -0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO E1162 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO E1162 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO E1162 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1500 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 394
        2.73 -     3.27: 8616
        3.27 -     3.82: 14326
        3.82 -     4.36: 16867
        4.36 -     4.90: 29330
  Nonbonded interactions: 69533
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E1088 "
            pdb=" OD1 ASP E1090 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" NH2 ARG E 660 "
            pdb=" O   ALA E1111 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   VAL E 418 "
            pdb=" OG1 THR E 421 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NH1 ARG E  50 "
            pdb=" OD2 ASP E 508 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   LEU E 267 "
            pdb=" ND2 ASN E 349 "
     model   vdw
     2.341 3.120
  ... (remaining 69528 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             18.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     24.890
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
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      :  0.002   0.028   8666  Z= 0.147
  Angle     :  0.479   7.774  11787  Z= 0.244
  Chirality :  0.040   0.129   1332
  Planarity :  0.004   0.038   1503
  Dihedral  : 12.229  83.878   3175
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  7.90 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.35 (0.27), residues: 1047
  helix:  1.75 (0.24), residues: 464
  sheet: -1.24 (0.41), residues: 160
  loop : -0.84 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 576 
 HIS   0.003   0.001   HIS E 531 
 PHE   0.008   0.001   PHE E 518 
 TYR   0.011   0.001   TYR E 517 
 ARG   0.009   0.000   ARG G 399 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.882 
Fit side-chains
REVERT: E   24 TRP cc_start: 0.8192 (m100) cc_final: 0.7908 (m100)
REVERT: E   97 LYS cc_start: 0.7945 (tptp) cc_final: 0.6645 (mttp)
REVERT: E  100 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7016 (tp30)
REVERT: E  140 ASN cc_start: 0.7453 (t0) cc_final: 0.7076 (m110)
REVERT: E  185 TRP cc_start: 0.6298 (m-10) cc_final: 0.5835 (m-10)
REVERT: E  254 MET cc_start: 0.6905 (tpt) cc_final: 0.6332 (ttt)
REVERT: E  301 ARG cc_start: 0.7539 (ptp-170) cc_final: 0.7311 (mtm110)
REVERT: E  311 GLU cc_start: 0.7235 (tp30) cc_final: 0.7030 (tp30)
REVERT: E  390 LEU cc_start: 0.8195 (pp) cc_final: 0.7494 (mt)
REVERT: E  396 ILE cc_start: 0.7753 (mm) cc_final: 0.7546 (mt)
REVERT: E  479 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8185 (mt)
REVERT: E  503 SER cc_start: 0.8851 (p) cc_final: 0.8540 (t)
REVERT: E  828 ASP cc_start: 0.7239 (m-30) cc_final: 0.6728 (m-30)
REVERT: E  992 PHE cc_start: 0.8036 (m-10) cc_final: 0.7798 (m-80)
REVERT: E 1243 MET cc_start: 0.6475 (tpp) cc_final: 0.6255 (tpp)
  outliers start: 17
  outliers final: 4
  residues processed: 174
  average time/residue: 0.2093
  time to fit residues: 50.2237
Evaluate side-chains
  135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  527 MET
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1207 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0770
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0470
   overall best weight:    0.3014

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

Flipped N/Q/H residues before XYZ refinement:
E  47 GLN
E 105 ASN
E 153 HIS
E 405 HIS
** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1003 GLN
** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.205818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.171049 restraints weight = 9385.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.35
r_work: 0.3677 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8666  Z= 0.227
  Angle     :  0.555  15.061  11787  Z= 0.276
  Chirality :  0.044   0.146   1332
  Planarity :  0.004   0.041   1503
  Dihedral  :  5.141  55.516   1155
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 10.03 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.13 (0.26), residues: 1047
  helix:  1.56 (0.24), residues: 472
  sheet: -1.52 (0.40), residues: 158
  loop : -0.93 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E 531 
 PHE   0.010   0.002   PHE E 518 
 TYR   0.019   0.001   TYR E 475 
 ARG   0.011   0.000   ARG E1237 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 1.114 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7862 (tptp) cc_final: 0.6822 (mttp)
REVERT: E  100 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6979 (tp30)
REVERT: E  128 ASP cc_start: 0.7226 (m-30) cc_final: 0.6867 (p0)
REVERT: E  140 ASN cc_start: 0.7465 (t0) cc_final: 0.7161 (m110)
REVERT: E  164 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7555 (m)
REVERT: E  182 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7776 (tt)
REVERT: E  186 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6317 (mmt)
REVERT: E  204 LYS cc_start: 0.7261 (mptt) cc_final: 0.6843 (tmmt)
REVERT: E  254 MET cc_start: 0.7313 (tpt) cc_final: 0.6654 (ttt)
REVERT: E  281 GLN cc_start: 0.7959 (mm110) cc_final: 0.7732 (mm-40)
REVERT: E  390 LEU cc_start: 0.8140 (pp) cc_final: 0.7617 (mt)
REVERT: E  479 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7969 (mt)
REVERT: E  483 SER cc_start: 0.8289 (m) cc_final: 0.8007 (p)
REVERT: E  503 SER cc_start: 0.8918 (p) cc_final: 0.8644 (t)
REVERT: E  557 ASN cc_start: 0.6638 (t0) cc_final: 0.6292 (t0)
REVERT: E  828 ASP cc_start: 0.7113 (m-30) cc_final: 0.6541 (m-30)
REVERT: E  992 PHE cc_start: 0.8078 (m-10) cc_final: 0.7860 (m-80)
REVERT: E 1004 GLN cc_start: 0.6965 (mt0) cc_final: 0.6631 (mt0)
REVERT: E 1022 ASN cc_start: 0.2331 (OUTLIER) cc_final: 0.1993 (m-40)
REVERT: E 1073 MET cc_start: 0.8197 (mtp) cc_final: 0.7353 (ttm)
REVERT: E 1154 ARG cc_start: 0.7237 (mtp-110) cc_final: 0.6934 (mtp-110)
REVERT: E 1238 ILE cc_start: 0.5022 (mt) cc_final: 0.4769 (mm)
REVERT: E 1243 MET cc_start: 0.6723 (tpp) cc_final: 0.6330 (tpp)
  outliers start: 28
  outliers final: 18
  residues processed: 176
  average time/residue: 0.2412
  time to fit residues: 58.4217
Evaluate side-chains
  163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  105 ASN
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  257 ASP
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  393 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  527 MET
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  588 PHE
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1025 VAL
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1306 CYS
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 69 optimal weight:    0.0980
   chunk 57 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 7 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0040
   overall best weight:    0.2792

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

Flipped N/Q/H residues before XYZ refinement:
E 405 HIS
E 565 GLN
** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1003 GLN
** E1159 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 = 0.4176 r_free = 0.4176 target = 0.203524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.168529 restraints weight = 9509.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 2.41
r_work: 0.3642 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8666  Z= 0.211
  Angle     :  0.518  10.533  11787  Z= 0.260
  Chirality :  0.043   0.140   1332
  Planarity :  0.004   0.042   1503
  Dihedral  :  5.025  53.308   1155
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 11.42 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1047
  helix:  1.58 (0.24), residues: 473
  sheet: -1.51 (0.40), residues: 157
  loop : -0.93 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E 531 
 PHE   0.009   0.001   PHE E 588 
 TYR   0.014   0.001   TYR E 475 
 ARG   0.003   0.000   ARG E1237 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.933 
Fit side-chains
REVERT: E   64 LEU cc_start: 0.8047 (mp) cc_final: 0.7793 (mp)
REVERT: E   97 LYS cc_start: 0.7902 (tptp) cc_final: 0.6886 (mttp)
REVERT: E  100 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6983 (tp30)
REVERT: E  128 ASP cc_start: 0.7260 (m-30) cc_final: 0.6900 (p0)
REVERT: E  140 ASN cc_start: 0.7443 (t0) cc_final: 0.7205 (m110)
REVERT: E  164 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7262 (p)
REVERT: E  182 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7813 (tt)
REVERT: E  186 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6582 (mmt)
REVERT: E  204 LYS cc_start: 0.7496 (mptt) cc_final: 0.7200 (tmmt)
REVERT: E  254 MET cc_start: 0.7448 (tpt) cc_final: 0.6768 (ttt)
REVERT: E  375 MET cc_start: 0.8566 (pmm) cc_final: 0.7679 (pmm)
REVERT: E  390 LEU cc_start: 0.8101 (pp) cc_final: 0.7604 (mt)
REVERT: E  479 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8115 (mt)
REVERT: E  483 SER cc_start: 0.8224 (m) cc_final: 0.7886 (p)
REVERT: E  503 SER cc_start: 0.8975 (p) cc_final: 0.8760 (t)
REVERT: E  557 ASN cc_start: 0.6970 (t0) cc_final: 0.6414 (t0)
REVERT: E  565 GLN cc_start: 0.7071 (mt0) cc_final: 0.6786 (mt0)
REVERT: E  603 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7407 (mtpt)
REVERT: E  641 ASP cc_start: 0.6890 (m-30) cc_final: 0.6106 (m-30)
REVERT: E  828 ASP cc_start: 0.7170 (m-30) cc_final: 0.6667 (m-30)
REVERT: E  992 PHE cc_start: 0.8078 (m-10) cc_final: 0.7844 (m-80)
REVERT: E  993 LEU cc_start: 0.8228 (mp) cc_final: 0.7871 (mp)
REVERT: E 1022 ASN cc_start: 0.2056 (OUTLIER) cc_final: 0.1584 (m-40)
REVERT: E 1145 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7827 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7009 (mtp-110)
REVERT: E 1190 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7048 (mt)
REVERT: E 1243 MET cc_start: 0.6882 (tpp) cc_final: 0.6524 (tpp)
REVERT: G  403 MET cc_start: 0.8720 (ttm) cc_final: 0.8209 (ttm)
  outliers start: 38
  outliers final: 22
  residues processed: 171
  average time/residue: 0.2170
  time to fit residues: 50.8524
Evaluate side-chains
  168 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 LEU
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  527 MET
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  588 PHE
Chi-restraints excluded: chain E residue  604 LEU
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue  839 TYR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1025 VAL
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1128 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1306 CYS
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 93 optimal weight:    0.4980
   chunk 88 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 103 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0970
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
E 105 ASN
E 405 HIS
E 956 GLN
** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1312 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.192342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.157390 restraints weight = 9522.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.39
r_work: 0.3529 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   8666  Z= 0.340
  Angle     :  0.612  10.264  11787  Z= 0.311
  Chirality :  0.046   0.145   1332
  Planarity :  0.005   0.045   1503
  Dihedral  :  5.325  58.320   1155
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 11.74 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.18 (0.26), residues: 1047
  helix:  1.36 (0.24), residues: 469
  sheet: -1.86 (0.39), residues: 156
  loop : -1.07 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP E1049 
 HIS   0.005   0.001   HIS E 531 
 PHE   0.019   0.002   PHE E1048 
 TYR   0.016   0.002   TYR E1328 
 ARG   0.005   0.001   ARG E1237 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 164
  time to evaluate  : 0.919 
Fit side-chains
REVERT: E   64 LEU cc_start: 0.8207 (mp) cc_final: 0.7976 (mp)
REVERT: E   97 LYS cc_start: 0.8084 (tptp) cc_final: 0.7128 (mttp)
REVERT: E  100 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7062 (tp30)
REVERT: E  128 ASP cc_start: 0.7497 (m-30) cc_final: 0.7144 (p0)
REVERT: E  139 ARG cc_start: 0.6578 (mtm-85) cc_final: 0.6182 (ttp-110)
REVERT: E  182 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7697 (tp)
REVERT: E  186 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7392 (mmt)
REVERT: E  301 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7888 (ptp90)
REVERT: E  375 MET cc_start: 0.8535 (pmm) cc_final: 0.7697 (pmm)
REVERT: E  390 LEU cc_start: 0.8010 (pp) cc_final: 0.7505 (mt)
REVERT: E  483 SER cc_start: 0.8405 (m) cc_final: 0.8114 (p)
REVERT: E  503 SER cc_start: 0.9002 (p) cc_final: 0.8728 (t)
REVERT: E  603 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8154 (mtpt)
REVERT: E  641 ASP cc_start: 0.7458 (m-30) cc_final: 0.6721 (m-30)
REVERT: E  828 ASP cc_start: 0.7314 (m-30) cc_final: 0.6867 (m-30)
REVERT: E  965 ARG cc_start: 0.8729 (ttm170) cc_final: 0.8491 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.3026 (OUTLIER) cc_final: 0.2628 (m-40)
REVERT: E 1127 MET cc_start: 0.8349 (ttt) cc_final: 0.8105 (ttt)
REVERT: E 1145 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7572 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7011 (mtp85)
REVERT: E 1193 TYR cc_start: 0.6346 (m-80) cc_final: 0.6140 (m-80)
REVERT: E 1243 MET cc_start: 0.6527 (tpp) cc_final: 0.6259 (tpp)
REVERT: E 1306 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6509 (p)
REVERT: G  403 MET cc_start: 0.8937 (ttm) cc_final: 0.8638 (ttm)
  outliers start: 41
  outliers final: 27
  residues processed: 191
  average time/residue: 0.2368
  time to fit residues: 61.1046
Evaluate side-chains
  176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 LEU
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  188 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  196 CYS
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue  956 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1025 VAL
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1042 ASP
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1144 VAL
Chi-restraints excluded: chain E residue 1182 VAL
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1306 CYS
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 85 optimal weight:    0.3980
   chunk 79 optimal weight:    0.4980
   chunk 93 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   chunk 77 optimal weight:    0.1980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
E 105 ASN
E 149 HIS
E 153 HIS
E 161 ASN
E 405 HIS
E1233 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.193624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.158693 restraints weight = 9422.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.38
r_work: 0.3533 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8666  Z= 0.250
  Angle     :  0.546   8.551  11787  Z= 0.276
  Chirality :  0.044   0.171   1332
  Planarity :  0.004   0.043   1503
  Dihedral  :  5.092  56.663   1152
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 13.02 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.12 (0.26), residues: 1047
  helix:  1.44 (0.24), residues: 470
  sheet: -2.00 (0.38), residues: 162
  loop : -0.98 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E 601 
 PHE   0.010   0.001   PHE E 350 
 TYR   0.015   0.001   TYR E 475 
 ARG   0.005   0.000   ARG E1203 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 143
  time to evaluate  : 0.870 
Fit side-chains
REVERT: E   64 LEU cc_start: 0.8110 (mp) cc_final: 0.7878 (mp)
REVERT: E   97 LYS cc_start: 0.8053 (tptp) cc_final: 0.7077 (mttm)
REVERT: E  100 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7035 (tp30)
REVERT: E  128 ASP cc_start: 0.7365 (m-30) cc_final: 0.6987 (p0)
REVERT: E  139 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6337 (ttp-110)
REVERT: E  143 GLU cc_start: 0.7022 (pm20) cc_final: 0.6816 (pm20)
REVERT: E  182 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7682 (tp)
REVERT: E  186 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7321 (mmt)
REVERT: E  375 MET cc_start: 0.8506 (pmm) cc_final: 0.7634 (pmm)
REVERT: E  390 LEU cc_start: 0.7981 (pp) cc_final: 0.7340 (mt)
REVERT: E  479 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8219 (mt)
REVERT: E  483 SER cc_start: 0.8395 (m) cc_final: 0.8109 (p)
REVERT: E  503 SER cc_start: 0.9004 (p) cc_final: 0.8743 (t)
REVERT: E  565 GLN cc_start: 0.7127 (mt0) cc_final: 0.6891 (mt0)
REVERT: E  593 TRP cc_start: 0.6791 (m-10) cc_final: 0.6308 (m-10)
REVERT: E  641 ASP cc_start: 0.7546 (m-30) cc_final: 0.7069 (m-30)
REVERT: E  828 ASP cc_start: 0.7301 (m-30) cc_final: 0.6879 (m-30)
REVERT: E  965 ARG cc_start: 0.8720 (ttm170) cc_final: 0.8481 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.2892 (OUTLIER) cc_final: 0.2515 (m-40)
REVERT: E 1127 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7981 (ttt)
REVERT: E 1145 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7432 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7616 (mtp-110) cc_final: 0.6911 (mtp85)
REVERT: E 1193 TYR cc_start: 0.6337 (m-80) cc_final: 0.6096 (m-80)
REVERT: E 1243 MET cc_start: 0.6688 (tpp) cc_final: 0.6310 (tpp)
REVERT: E 1306 CYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6538 (p)
REVERT: G  403 MET cc_start: 0.8924 (ttm) cc_final: 0.8713 (ttm)
  outliers start: 40
  outliers final: 24
  residues processed: 164
  average time/residue: 0.2304
  time to fit residues: 51.1543
Evaluate side-chains
  166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 LEU
Chi-restraints excluded: chain E residue  105 ASN
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  295 ILE
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  541 VAL
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  646 MET
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1042 ASP
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1127 MET
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1144 VAL
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1306 CYS
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0060
   chunk 13 optimal weight:    0.0870
   chunk 85 optimal weight:    0.0670
   chunk 80 optimal weight:    0.0170
   chunk 58 optimal weight:    0.1980
   chunk 15 optimal weight:    0.1980
   chunk 61 optimal weight:    0.2980
   chunk 94 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.0750

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

Flipped N/Q/H residues before XYZ refinement:
E  47 GLN
E 405 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.197399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.163060 restraints weight = 9339.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.36
r_work: 0.3587 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8666  Z= 0.148
  Angle     :  0.496   8.154  11787  Z= 0.250
  Chirality :  0.042   0.175   1332
  Planarity :  0.004   0.040   1503
  Dihedral  :  4.882  56.415   1152
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 14.09 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.11 (0.26), residues: 1047
  helix:  1.62 (0.24), residues: 478
  sheet: -1.86 (0.40), residues: 157
  loop : -0.91 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP E1049 
 HIS   0.003   0.001   HIS E 531 
 PHE   0.008   0.001   PHE E 626 
 TYR   0.014   0.001   TYR E 475 
 ARG   0.003   0.000   ARG E 301 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 0.862 
Fit side-chains
REVERT: E   64 LEU cc_start: 0.8073 (mp) cc_final: 0.7870 (mp)
REVERT: E   97 LYS cc_start: 0.8134 (tptp) cc_final: 0.7208 (mttm)
REVERT: E  100 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7069 (tp30)
REVERT: E  139 ARG cc_start: 0.6724 (mtm-85) cc_final: 0.6298 (ttp-110)
REVERT: E  182 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7699 (tp)
REVERT: E  186 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7107 (mmt)
REVERT: E  375 MET cc_start: 0.8537 (pmm) cc_final: 0.7634 (pmm)
REVERT: E  378 MET cc_start: 0.8115 (tpp) cc_final: 0.7600 (tpp)
REVERT: E  390 LEU cc_start: 0.7908 (pp) cc_final: 0.7435 (mt)
REVERT: E  479 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8173 (mt)
REVERT: E  483 SER cc_start: 0.8352 (m) cc_final: 0.8094 (p)
REVERT: E  503 SER cc_start: 0.8976 (p) cc_final: 0.8745 (t)
REVERT: E  557 ASN cc_start: 0.6868 (t0) cc_final: 0.6265 (t0)
REVERT: E  593 TRP cc_start: 0.6810 (m-10) cc_final: 0.6322 (m-10)
REVERT: E  598 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7807 (m-30)
REVERT: E  641 ASP cc_start: 0.7461 (m-30) cc_final: 0.6963 (m-30)
REVERT: E  673 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6411 (tp40)
REVERT: E  828 ASP cc_start: 0.7310 (m-30) cc_final: 0.6865 (m-30)
REVERT: E  965 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8418 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.3005 (OUTLIER) cc_final: 0.2682 (m-40)
REVERT: E 1052 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6499 (mm-30)
REVERT: E 1127 MET cc_start: 0.8133 (ttt) cc_final: 0.7857 (ttt)
REVERT: E 1145 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7467 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7434 (mtp-110) cc_final: 0.7142 (ptp90)
REVERT: E 1243 MET cc_start: 0.6204 (tpp) cc_final: 0.5915 (tpp)
REVERT: E 1256 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6517 (tt)
REVERT: E 1306 CYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6540 (p)
REVERT: G  403 MET cc_start: 0.8855 (ttm) cc_final: 0.8232 (ttm)
  outliers start: 34
  outliers final: 21
  residues processed: 162
  average time/residue: 0.2305
  time to fit residues: 50.2952
Evaluate side-chains
  162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  295 ILE
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  588 PHE
Chi-restraints excluded: chain E residue  598 ASP
Chi-restraints excluded: chain E residue  604 LEU
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1083 LEU
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1191 ARG
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1256 LEU
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1306 CYS
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0970
   chunk 31 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0870
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
E 105 ASN
E 405 HIS
E 513 ASN
E 565 GLN
E 956 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.178660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.146485 restraints weight = 9260.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.15
r_work: 0.3403 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8666  Z= 0.256
  Angle     :  0.538   8.226  11787  Z= 0.270
  Chirality :  0.044   0.171   1332
  Planarity :  0.004   0.041   1503
  Dihedral  :  4.895  49.656   1152
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 14.30 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.06 (0.26), residues: 1047
  helix:  1.58 (0.24), residues: 475
  sheet: -1.90 (0.40), residues: 157
  loop : -0.93 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E 531 
 PHE   0.011   0.001   PHE E 350 
 TYR   0.013   0.001   TYR E 475 
 ARG   0.007   0.000   ARG E 985 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 1.037 
Fit side-chains
REVERT: E   64 LEU cc_start: 0.8063 (mp) cc_final: 0.7852 (mp)
REVERT: E   97 LYS cc_start: 0.7956 (tptp) cc_final: 0.6966 (mttp)
REVERT: E  100 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7010 (tp30)
REVERT: E  139 ARG cc_start: 0.6718 (mtm-85) cc_final: 0.6058 (ttp-110)
REVERT: E  182 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7747 (tp)
REVERT: E  186 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7330 (mmt)
REVERT: E  375 MET cc_start: 0.8489 (pmm) cc_final: 0.7526 (pmm)
REVERT: E  378 MET cc_start: 0.8243 (tpp) cc_final: 0.7705 (tpp)
REVERT: E  390 LEU cc_start: 0.7754 (pp) cc_final: 0.7274 (mt)
REVERT: E  479 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8018 (mt)
REVERT: E  483 SER cc_start: 0.8296 (m) cc_final: 0.8027 (p)
REVERT: E  503 SER cc_start: 0.8874 (p) cc_final: 0.8585 (t)
REVERT: E  593 TRP cc_start: 0.6702 (m-10) cc_final: 0.6164 (m-10)
REVERT: E  627 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (t)
REVERT: E  641 ASP cc_start: 0.7547 (m-30) cc_final: 0.6998 (m-30)
REVERT: E  673 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6317 (tp40)
REVERT: E  828 ASP cc_start: 0.7334 (m-30) cc_final: 0.6905 (m-30)
REVERT: E  965 ARG cc_start: 0.8406 (ttm170) cc_final: 0.8186 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.2746 (OUTLIER) cc_final: 0.2263 (m-40)
REVERT: E 1052 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6421 (mm-30)
REVERT: E 1127 MET cc_start: 0.8260 (ttt) cc_final: 0.8003 (ttt)
REVERT: E 1145 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7306 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.6956 (ptp90)
REVERT: E 1243 MET cc_start: 0.6372 (tpp) cc_final: 0.5959 (tpp)
REVERT: G  403 MET cc_start: 0.8808 (ttm) cc_final: 0.8168 (ttm)
  outliers start: 41
  outliers final: 28
  residues processed: 165
  average time/residue: 0.2267
  time to fit residues: 50.6650
Evaluate side-chains
  170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  188 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  295 ILE
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  627 VAL
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue  955 VAL
Chi-restraints excluded: chain E residue  956 GLN
Chi-restraints excluded: chain E residue  980 LEU
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1042 ASP
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1083 LEU
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1144 VAL
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1191 ARG
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 49 optimal weight:    0.3980
   chunk 80 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0970
   chunk 8 optimal weight:    0.1980
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0870
   chunk 74 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   overall best weight:    0.1756

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

Flipped N/Q/H residues before XYZ refinement:
E 105 ASN
E 405 HIS
E 956 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.174726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.142374 restraints weight = 9449.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.13
r_work: 0.3378 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8666  Z= 0.177
  Angle     :  0.514   9.489  11787  Z= 0.256
  Chirality :  0.042   0.161   1332
  Planarity :  0.004   0.041   1503
  Dihedral  :  4.807  48.561   1152
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 14.94 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.14 (0.27), residues: 1047
  helix:  1.66 (0.24), residues: 476
  sheet: -1.84 (0.39), residues: 162
  loop : -0.89 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP E1049 
 HIS   0.003   0.001   HIS E 531 
 PHE   0.009   0.001   PHE E 350 
 TYR   0.013   0.001   TYR E 475 
 ARG   0.007   0.000   ARG E1203 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.887 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7951 (tptp) cc_final: 0.6968 (mttp)
REVERT: E  100 GLU cc_start: 0.7660 (mt-10) cc_final: 0.6981 (tp30)
REVERT: E  139 ARG cc_start: 0.6707 (mtm-85) cc_final: 0.6064 (ttp-110)
REVERT: E  143 GLU cc_start: 0.7210 (pm20) cc_final: 0.6895 (pm20)
REVERT: E  182 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7750 (tp)
REVERT: E  186 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7267 (mmt)
REVERT: E  375 MET cc_start: 0.8508 (pmm) cc_final: 0.7579 (pmm)
REVERT: E  378 MET cc_start: 0.8172 (tpp) cc_final: 0.7626 (tpp)
REVERT: E  390 LEU cc_start: 0.7727 (pp) cc_final: 0.7286 (mt)
REVERT: E  479 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7984 (mt)
REVERT: E  483 SER cc_start: 0.8280 (m) cc_final: 0.8025 (p)
REVERT: E  503 SER cc_start: 0.8769 (p) cc_final: 0.8495 (t)
REVERT: E  593 TRP cc_start: 0.6690 (m-10) cc_final: 0.6195 (m-10)
REVERT: E  598 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7552 (m-30)
REVERT: E  627 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7990 (t)
REVERT: E  641 ASP cc_start: 0.7524 (m-30) cc_final: 0.6517 (m-30)
REVERT: E  673 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6434 (tp40)
REVERT: E  828 ASP cc_start: 0.7289 (m-30) cc_final: 0.6863 (m-30)
REVERT: E  965 ARG cc_start: 0.8274 (ttm170) cc_final: 0.8057 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.2686 (OUTLIER) cc_final: 0.2247 (m-40)
REVERT: E 1052 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6482 (mm-30)
REVERT: E 1127 MET cc_start: 0.8227 (ttt) cc_final: 0.7979 (ttt)
REVERT: E 1145 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7293 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7348 (mtp-110) cc_final: 0.7020 (ptp90)
REVERT: E 1238 ILE cc_start: 0.5923 (mp) cc_final: 0.5697 (mp)
REVERT: E 1243 MET cc_start: 0.6407 (tpp) cc_final: 0.5981 (tpp)
REVERT: G  403 MET cc_start: 0.8776 (ttm) cc_final: 0.8184 (ttm)
  outliers start: 38
  outliers final: 27
  residues processed: 162
  average time/residue: 0.2260
  time to fit residues: 50.0157
Evaluate side-chains
  168 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  105 ASN
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  188 SER
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  295 ILE
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  541 VAL
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  598 ASP
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  627 VAL
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue  980 LEU
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1042 ASP
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1083 LEU
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1144 VAL
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1191 ARG
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1253 VAL
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0370
   chunk 12 optimal weight:    0.0370
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
E 105 ASN
E 405 HIS
E 565 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.173879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.141496 restraints weight = 9529.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.11
r_work: 0.3361 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8666  Z= 0.240
  Angle     :  0.542   9.154  11787  Z= 0.270
  Chirality :  0.043   0.169   1332
  Planarity :  0.004   0.040   1503
  Dihedral  :  4.808  44.491   1152
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.47 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.13 (0.27), residues: 1047
  helix:  1.69 (0.24), residues: 463
  sheet: -1.94 (0.39), residues: 162
  loop : -0.84 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E 531 
 PHE   0.010   0.001   PHE E 350 
 TYR   0.013   0.001   TYR E 839 
 ARG   0.007   0.000   ARG E1203 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 1.050 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7945 (tptp) cc_final: 0.6935 (mttp)
REVERT: E  100 GLU cc_start: 0.7709 (mt-10) cc_final: 0.6943 (tp30)
REVERT: E  139 ARG cc_start: 0.6514 (mtm-85) cc_final: 0.5971 (ttp-110)
REVERT: E  143 GLU cc_start: 0.7221 (pm20) cc_final: 0.6932 (pm20)
REVERT: E  182 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7856 (tp)
REVERT: E  375 MET cc_start: 0.8461 (pmm) cc_final: 0.7689 (pmm)
REVERT: E  378 MET cc_start: 0.8183 (tpp) cc_final: 0.7622 (tpp)
REVERT: E  390 LEU cc_start: 0.7657 (pp) cc_final: 0.7202 (mt)
REVERT: E  479 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7932 (mt)
REVERT: E  483 SER cc_start: 0.8289 (m) cc_final: 0.8037 (p)
REVERT: E  503 SER cc_start: 0.8828 (p) cc_final: 0.8574 (t)
REVERT: E  593 TRP cc_start: 0.6657 (m-10) cc_final: 0.6129 (m-10)
REVERT: E  627 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7974 (t)
REVERT: E  641 ASP cc_start: 0.7513 (m-30) cc_final: 0.6524 (m-30)
REVERT: E  673 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6428 (tp40)
REVERT: E  828 ASP cc_start: 0.7276 (m-30) cc_final: 0.6848 (m-30)
REVERT: E  965 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7963 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.2620 (OUTLIER) cc_final: 0.2095 (m-40)
REVERT: E 1052 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6481 (mm-30)
REVERT: E 1127 MET cc_start: 0.8222 (ttt) cc_final: 0.7921 (ttt)
REVERT: E 1145 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7262 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7342 (mtp-110) cc_final: 0.7013 (ptp90)
REVERT: E 1238 ILE cc_start: 0.6214 (mp) cc_final: 0.5992 (mp)
REVERT: E 1243 MET cc_start: 0.6198 (tpp) cc_final: 0.5769 (tpp)
REVERT: E 1280 TYR cc_start: 0.6994 (m-80) cc_final: 0.6676 (m-80)
REVERT: G  403 MET cc_start: 0.8769 (ttm) cc_final: 0.8236 (ttm)
  outliers start: 39
  outliers final: 27
  residues processed: 159
  average time/residue: 0.2318
  time to fit residues: 50.2565
Evaluate side-chains
  163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 LEU
Chi-restraints excluded: chain E residue  105 ASN
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  188 SER
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  295 ILE
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  541 VAL
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  627 VAL
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue  980 LEU
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1042 ASP
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1083 LEU
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1146 ILE
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1191 ARG
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1253 VAL
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.0980
   chunk 36 optimal weight:    0.0050
   chunk 91 optimal weight:    0.9990
   chunk 88 optimal weight:    0.4980
   chunk 101 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    0.4980
   chunk 61 optimal weight:    0.4980
   chunk 79 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
E 105 ASN
** E1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.175507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.142426 restraints weight = 9266.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.25
r_work: 0.3316 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8666  Z= 0.225
  Angle     :  0.532   9.052  11787  Z= 0.265
  Chirality :  0.043   0.166   1332
  Planarity :  0.004   0.042   1503
  Dihedral  :  4.791  44.364   1152
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 15.37 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.08 (0.27), residues: 1047
  helix:  1.68 (0.24), residues: 464
  sheet: -2.07 (0.37), residues: 173
  loop : -0.80 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E 531 
 PHE   0.009   0.001   PHE E 350 
 TYR   0.013   0.001   TYR E 475 
 ARG   0.007   0.000   ARG E1203 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.987 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.8071 (tptp) cc_final: 0.7161 (mttp)
REVERT: E  100 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7026 (tp30)
REVERT: E  139 ARG cc_start: 0.6537 (mtm-85) cc_final: 0.6114 (ttp-110)
REVERT: E  143 GLU cc_start: 0.7025 (pm20) cc_final: 0.6812 (pm20)
REVERT: E  182 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7876 (tp)
REVERT: E  375 MET cc_start: 0.8485 (pmm) cc_final: 0.7557 (pmm)
REVERT: E  378 MET cc_start: 0.8174 (tpp) cc_final: 0.7634 (tpp)
REVERT: E  390 LEU cc_start: 0.7854 (pp) cc_final: 0.7447 (mt)
REVERT: E  479 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8115 (mt)
REVERT: E  483 SER cc_start: 0.8271 (m) cc_final: 0.8027 (p)
REVERT: E  503 SER cc_start: 0.8950 (p) cc_final: 0.8688 (t)
REVERT: E  593 TRP cc_start: 0.6861 (m-10) cc_final: 0.6354 (m-10)
REVERT: E  598 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7566 (m-30)
REVERT: E  641 ASP cc_start: 0.7657 (m-30) cc_final: 0.6768 (m-30)
REVERT: E  673 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6645 (tp40)
REVERT: E  828 ASP cc_start: 0.7300 (m-30) cc_final: 0.6861 (m-30)
REVERT: E  965 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8221 (ttm-80)
REVERT: E 1022 ASN cc_start: 0.2858 (OUTLIER) cc_final: 0.2364 (m-40)
REVERT: E 1052 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6383 (mt-10)
REVERT: E 1127 MET cc_start: 0.8270 (ttt) cc_final: 0.7897 (ttt)
REVERT: E 1145 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7411 (mmt180)
REVERT: E 1154 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7199 (ptp90)
REVERT: E 1238 ILE cc_start: 0.6273 (mp) cc_final: 0.6046 (mp)
REVERT: E 1243 MET cc_start: 0.6109 (tpp) cc_final: 0.5868 (tpp)
REVERT: E 1280 TYR cc_start: 0.6802 (m-80) cc_final: 0.6508 (m-80)
REVERT: G  403 MET cc_start: 0.8887 (ttm) cc_final: 0.8339 (ttm)
  outliers start: 36
  outliers final: 28
  residues processed: 157
  average time/residue: 0.2396
  time to fit residues: 50.9171
Evaluate side-chains
  166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 LEU
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  188 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  295 ILE
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  541 VAL
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  598 ASP
Chi-restraints excluded: chain E residue  609 SER
Chi-restraints excluded: chain E residue  673 GLN
Chi-restraints excluded: chain E residue  956 GLN
Chi-restraints excluded: chain E residue  980 LEU
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1022 ASN
Chi-restraints excluded: chain E residue 1028 VAL
Chi-restraints excluded: chain E residue 1042 ASP
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1083 LEU
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1141 SER
Chi-restraints excluded: chain E residue 1190 ILE
Chi-restraints excluded: chain E residue 1191 ARG
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1253 VAL
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1330 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 86 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
E 565 GLN
** E1159 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 = 0.3736 r_free = 0.3736 target = 0.163124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.130832 restraints weight = 9735.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.18
r_work: 0.3211 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   8666  Z= 0.408
  Angle     :  0.645   8.943  11787  Z= 0.326
  Chirality :  0.048   0.200   1332
  Planarity :  0.005   0.052   1503
  Dihedral  :  5.239  42.961   1152
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.69 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.33 (0.26), residues: 1047
  helix:  1.32 (0.24), residues: 464
  sheet: -2.23 (0.37), residues: 166
  loop : -1.05 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP E1049 
 HIS   0.005   0.001   HIS E1210 
 PHE   0.016   0.002   PHE E1048 
 TYR   0.015   0.002   TYR E1059 
 ARG   0.009   0.001   ARG E1203 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4552.50 seconds
wall clock time: 82 minutes 13.29 seconds (4933.29 seconds total)