Starting phenix.real_space_refine
on Wed Jan 15 15:50:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f43_50182/01_2025/9f43_50182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f43_50182/01_2025/9f43_50182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f43_50182/01_2025/9f43_50182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f43_50182/01_2025/9f43_50182.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f43_50182/01_2025/9f43_50182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f43_50182/01_2025/9f43_50182.cif"
  }
  resolution = 3.49
  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=   0.027
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 32 residue(s): 0.02s

  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: 3.07, per 1000 atoms: 0.36
  Number of scatterers: 8465
  At special positions: 0
  Unit cell: (102.18, 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: 2.47
  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:
      41 helices and 9 sheets defined
      47.8% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'E' and resid 19 through 25
      removed outlier: 3.793A  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: 3.533A  pdb=" N   ILE E 202 " --> pdb=" O   ASN E 198 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU E 218 " --> pdb=" O   GLU E 214 " (cutoff:3.500A)
      removed outlier: 4.245A  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 280
    Processing helix  chain 'E' and resid 281 through 287
    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: 3.540A  pdb=" N   ARG E 338 " --> pdb=" O   GLN E 334 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 359
      removed outlier: 3.784A  pdb=" N   LEU E 352 " --> pdb=" O   ARG E 348 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER E 359 " --> pdb=" O   ARG E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 377 through 391
      removed outlier: 3.644A  pdb=" N   ALA E 381 " --> pdb=" O   ALA E 377 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 392 through 398
    Processing helix  chain 'E' and resid 407 through 422
      removed outlier: 3.797A  pdb=" N   MET E 422 " --> pdb=" O   VAL E 418 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 432 through 442
      removed outlier: 3.788A  pdb=" N   LEU E 441 " --> pdb=" O   LEU E 437 " (cutoff:3.500A)
      removed outlier: 4.236A  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 480
      removed outlier: 3.695A  pdb=" N   LEU E 480 " --> pdb=" O   VAL E 476 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 484 through 486
      No H-bonds generated for 'chain 'E' and resid 484 through 486'
    Processing helix  chain 'E' and resid 487 through 502
    Processing helix  chain 'E' and resid 504 through 512
      removed outlier: 4.558A  pdb=" N   ASP E 508 " --> pdb=" O   SER E 504 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 513 through 523
      removed outlier: 4.007A  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: 3.606A  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 650
      removed outlier: 3.564A  pdb=" N   GLN E 650 " --> pdb=" O   MET E 646 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 656 through 674
    Processing helix  chain 'E' and resid 674 through 685
      removed outlier: 3.691A  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: 3.516A  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 969
      removed outlier: 3.836A  pdb=" N   TYR E 966 " --> pdb=" O   TRP E 962 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   PHE E 967 " --> pdb=" O   SER E 963 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA E 968 " --> pdb=" O   ALA E 964 " (cutoff:3.500A)
    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: 7.403A  pdb=" N   VAL E  58 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   LYS E 120 " --> pdb=" O   VAL E  58 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   VAL E  60 " --> pdb=" O   LYS E 120 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   SER E 122 " --> pdb=" O   VAL E  60 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU E  62 " --> pdb=" O   SER E 122 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ARG E 145 " --> pdb=" O   THR E  57 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   SER E  59 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL E 146 " --> pdb=" O   ILE E 191 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   VAL E 193 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   PHE E 148 " --> pdb=" O   VAL E 193 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   ASP E 195 " --> pdb=" O   PHE E 148 " (cutoff:3.500A)
      removed outlier: 6.633A  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: 3.953A  pdb=" N   ASP E1015 " --> pdb=" O   SER E1329 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   SER E1329 " --> pdb=" O   ASP E1015 " (cutoff:3.500A)
      removed outlier: 3.749A  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: 3.728A  pdb=" N   VAL E1028 " --> pdb=" O   ALA E1041 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ILE E1046 " --> pdb=" O   TYR E1059 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   TYR E1059 " --> pdb=" O   ILE E1046 " (cutoff:3.500A)
      removed outlier: 6.733A  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: 4.318A  pdb=" N   ALA E1092 " --> pdb=" O   THR E1088 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE E1093 " --> pdb=" O   ALA E1111 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ALA E1111 " --> pdb=" O   ILE E1093 " (cutoff:3.500A)
      removed outlier: 6.812A  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: 4.694A  pdb=" N   GLY E1142 " --> pdb=" O   ILE E1146 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   ILE E1146 " --> pdb=" O   GLY E1142 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL E1147 " --> pdb=" O   ASP E1160 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASP E1160 " --> pdb=" O   VAL E1147 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ILE E1149 " --> pdb=" O   VAL E1158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 1169 through 1173
      removed outlier: 6.959A  pdb=" N   ILE E1190 " --> pdb=" O   THR E1206 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   THR E1206 " --> pdb=" O   ILE E1190 " (cutoff:3.500A)
      removed outlier: 7.016A  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: 7.068A  pdb=" N   VAL E1230 " --> pdb=" O   VAL E1215 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ALA E1217 " --> pdb=" O   VAL E1228 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   VAL E1228 " --> pdb=" O   ALA E1217 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER E1229 " --> pdb=" O   ARG E1237 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER E1231 " --> pdb=" O   ASP E1235 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ASP E1235 " --> pdb=" O   SER E1231 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN E1248 " --> pdb=" O   ILE E1238 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ASP E1240 " --> pdb=" O   SER E1246 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   SER E1246 " --> pdb=" O   ASP E1240 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 1259 through 1261
      removed outlier: 3.513A  pdb=" N   ALA E1278 " --> pdb=" O   CYS E1270 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASN E1288 " --> pdb=" O   ILE E1279 " (cutoff:3.500A)

    406 hydrogen bonds defined for protein.
    1161 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: 3.09

  Time building geometry restraints manager: 2.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2764
        1.34 -     1.46: 1613
        1.46 -     1.58: 4204
        1.58 -     1.69: 0
        1.69 -     1.81: 85
  Bond restraints: 8666
  Sorted by residual:
  bond pdb=" N   VAL G 406 "
       pdb=" CA  VAL G 406 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.016 1.57e-02 4.06e+03 1.08e+00
  bond pdb=" CA  TYR E 839 "
       pdb=" CB  TYR E 839 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.011 1.31e-02 5.83e+03 6.56e-01
  bond pdb=" CB  ASN E 557 "
       pdb=" CG  ASN E 557 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.51e-01
  bond pdb=" CA  VAL G 406 "
       pdb=" CB  VAL G 406 "
    ideal  model  delta    sigma   weight residual
    1.532  1.543 -0.011 1.42e-02 4.96e+03 6.07e-01
  bond pdb=" C   ALA E1125 "
       pdb=" N   GLY E1126 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.011 1.46e-02 4.69e+03 5.76e-01
  ... (remaining 8661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 11505
        1.31 -     2.61: 212
        2.61 -     3.92: 60
        3.92 -     5.23: 8
        5.23 -     6.53: 2
  Bond angle restraints: 11787
  Sorted by residual:
  angle pdb=" CA  TYR E 839 "
        pdb=" CB  TYR E 839 "
        pdb=" CG  TYR E 839 "
      ideal   model   delta    sigma   weight residual
     113.90  120.43   -6.53 1.80e+00 3.09e-01 1.32e+01
  angle pdb=" N   VAL G 406 "
        pdb=" CA  VAL G 406 "
        pdb=" C   VAL G 406 "
      ideal   model   delta    sigma   weight residual
     106.21  108.54   -2.33 1.07e+00 8.73e-01 4.74e+00
  angle pdb=" N   PRO E 407 "
        pdb=" CA  PRO E 407 "
        pdb=" C   PRO E 407 "
      ideal   model   delta    sigma   weight residual
     114.92  112.40    2.52 1.19e+00 7.06e-01 4.47e+00
  angle pdb=" C   TYR E 839 "
        pdb=" CA  TYR E 839 "
        pdb=" CB  TYR E 839 "
      ideal   model   delta    sigma   weight residual
     111.50  114.21   -2.71 1.29e+00 6.01e-01 4.42e+00
  angle pdb=" CB  LYS E1056 "
        pdb=" CG  LYS E1056 "
        pdb=" CD  LYS E1056 "
      ideal   model   delta    sigma   weight residual
     111.30  115.45   -4.15 2.30e+00 1.89e-01 3.25e+00
  ... (remaining 11782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4670
       17.56 -    35.13: 415
       35.13 -    52.69: 97
       52.69 -    70.25: 15
       70.25 -    87.82: 8
  Dihedral angle restraints: 5205
    sinusoidal: 2092
      harmonic: 3113
  Sorted by residual:
  dihedral pdb=" CA  ASP E1042 "
           pdb=" CB  ASP E1042 "
           pdb=" CG  ASP E1042 "
           pdb=" OD1 ASP E1042 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.48   58.48     1      2.00e+01 2.50e-03 1.15e+01
  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  164.01   15.99     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLN E 242 "
           pdb=" CB  GLN E 242 "
           pdb=" CG  GLN E 242 "
           pdb=" CD  GLN E 242 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.65   57.35     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 5202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 838
       0.028 -    0.056: 305
       0.056 -    0.084: 104
       0.084 -    0.112: 61
       0.112 -    0.140: 24
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CG  LEU E 667 "
            pdb=" CB  LEU E 667 "
            pdb=" CD1 LEU E 667 "
            pdb=" CD2 LEU E 667 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ILE E1146 "
            pdb=" N   ILE E1146 "
            pdb=" C   ILE E1146 "
            pdb=" CB  ILE E1146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  VAL E1192 "
            pdb=" N   VAL E1192 "
            pdb=" C   VAL E1192 "
            pdb=" CB  VAL E1192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  ... (remaining 1329 not shown)

  Planarity restraints: 1503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 213 "    0.186 9.50e-02 1.11e+02   8.38e-02 5.01e+00
        pdb=" NE  ARG E 213 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 213 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 213 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 213 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E1243 "   -0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO E1244 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO E1244 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E1244 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E 527 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO E 528 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO E 528 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 528 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1500 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 112
        2.64 -     3.20: 7897
        3.20 -     3.77: 13218
        3.77 -     4.33: 17952
        4.33 -     4.90: 29896
  Nonbonded interactions: 69075
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E  89 "
            pdb=" OG  SER E  92 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" OG1 THR E1071 "
            pdb=" O   MET E1127 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" NH2 ARG E 660 "
            pdb=" O   ALA E1111 "
     model   vdw
     2.141 3.120
  nonbonded pdb=" OD1 ASN E 170 "
            pdb=" OG1 THR E 172 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   THR E 264 "
            pdb=" OG1 THR E 268 "
     model   vdw
     2.177 3.040
  ... (remaining 69070 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:             21.980
  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:                     24.720
  Find NCS groups from input model:        0.090
  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:             0.010
  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:   49.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
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   0.030   8666  Z= 0.145
  Angle     :  0.490   6.534  11787  Z= 0.257
  Chirality :  0.040   0.140   1332
  Planarity :  0.004   0.084   1503
  Dihedral  : 14.266  87.817   3175
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 15.90 %
    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:  1.09 (0.27), residues: 1047
  helix:  2.48 (0.25), residues: 465
  sheet: -1.11 (0.40), residues: 153
  loop : -0.52 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E1051 
 HIS   0.003   0.001   HIS E1061 
 PHE   0.010   0.001   PHE E 626 
 TYR   0.009   0.001   TYR E 808 
 ARG   0.015   0.000   ARG E 213 

*********************** 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
  128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9029 (tpp) cc_final: 0.8701 (tpp)
REVERT: E  242 GLN cc_start: 0.8394 (mt0) cc_final: 0.7933 (mp10)
REVERT: E  339 GLN cc_start: 0.8495 (tp40) cc_final: 0.8142 (tp-100)
REVERT: E  593 TRP cc_start: 0.7434 (m-10) cc_final: 0.6594 (m-90)
REVERT: E 1323 TYR cc_start: 0.6919 (m-10) cc_final: 0.6660 (m-10)
REVERT: G  403 MET cc_start: 0.6463 (ttm) cc_final: 0.6262 (ttp)
  outliers start: 2
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2302
  time to fit residues: 40.3928
Evaluate side-chains
  114 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  164 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0270
   chunk 53 optimal weight:    0.0020
   chunk 42 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0970
   overall best weight:    0.2044

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

Flipped N/Q/H residues before XYZ refinement:
E 153 HIS
E 326 ASN
E1113 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.171075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.142231 restraints weight = 11432.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.68
r_work: 0.3504 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8666  Z= 0.179
  Angle     :  0.508   7.493  11787  Z= 0.263
  Chirality :  0.042   0.204   1332
  Planarity :  0.004   0.046   1503
  Dihedral  :  3.739  24.888   1147
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.02 %
    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:  0.92 (0.27), residues: 1047
  helix:  2.31 (0.24), residues: 472
  sheet: -1.35 (0.39), residues: 158
  loop : -0.54 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1051 
 HIS   0.005   0.001   HIS E 531 
 PHE   0.011   0.001   PHE E 588 
 TYR   0.012   0.001   TYR E 517 
 ARG   0.007   0.000   ARG E1178 

*********************** 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
  149 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   63 VAL cc_start: 0.8643 (t) cc_final: 0.8441 (m)
REVERT: E  475 TYR cc_start: 0.6824 (m-80) cc_final: 0.6578 (m-80)
REVERT: G  403 MET cc_start: 0.6422 (ttm) cc_final: 0.6115 (ttp)
  outliers start: 23
  outliers final: 8
  residues processed: 138
  average time/residue: 0.1897
  time to fit residues: 37.3260
Evaluate side-chains
  116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
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:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0040
   chunk 7 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
E 198 ASN
E 326 ASN
** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 547 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.160654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.136823 restraints weight = 11523.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.04
r_work: 0.3470 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8666  Z= 0.283
  Angle     :  0.554  11.783  11787  Z= 0.284
  Chirality :  0.044   0.161   1332
  Planarity :  0.004   0.040   1503
  Dihedral  :  3.973  30.630   1147
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.72 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 13.77 %
    Favored  : 82.82 %
  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:  0.68 (0.27), residues: 1047
  helix:  2.12 (0.24), residues: 471
  sheet: -1.55 (0.38), residues: 168
  loop : -0.59 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1049 
 HIS   0.007   0.001   HIS E1262 
 PHE   0.015   0.002   PHE E 626 
 TYR   0.017   0.002   TYR E 475 
 ARG   0.003   0.000   ARG E 330 

*********************** 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
  162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9214 (tpp) cc_final: 0.8637 (mpp)
REVERT: E   52 LYS cc_start: 0.6354 (mmtm) cc_final: 0.6119 (mmtm)
REVERT: E   55 MET cc_start: 0.8468 (mmm) cc_final: 0.8116 (mmp)
REVERT: E  123 LEU cc_start: 0.8723 (mt) cc_final: 0.8379 (mp)
REVERT: E  475 TYR cc_start: 0.7153 (m-80) cc_final: 0.6891 (m-80)
REVERT: E  479 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8819 (mm)
REVERT: E  512 ASP cc_start: 0.7817 (t70) cc_final: 0.7232 (t0)
REVERT: E 1146 ILE cc_start: 0.8226 (mt) cc_final: 0.7719 (pt)
REVERT: E 1172 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: E 1323 TYR cc_start: 0.7078 (m-10) cc_final: 0.6612 (m-10)
REVERT: G  403 MET cc_start: 0.6894 (ttm) cc_final: 0.6573 (ttp)
  outliers start: 32
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1911
  time to fit residues: 40.6932
Evaluate side-chains
  126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  413 LEU
Chi-restraints excluded: chain E residue  444 VAL
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  651 LEU
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  836 SER
Chi-restraints excluded: chain E residue 1025 VAL
Chi-restraints excluded: chain E residue 1038 ILE
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1172 LEU
Chi-restraints excluded: chain E residue 1197 MET
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:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 101 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0470
   chunk 88 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 103 optimal weight:    0.0470
   chunk 73 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
E 114 GLN
E 326 ASN
** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1315 HIS

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 = 0.162768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.140958 restraints weight = 11434.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.85
r_work: 0.3504 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2005

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= 0.210
  Angle     :  0.518   8.979  11787  Z= 0.265
  Chirality :  0.043   0.161   1332
  Planarity :  0.004   0.038   1503
  Dihedral  :  3.853  20.462   1146
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 14.73 %
    Favored  : 81.64 %
  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:  0.69 (0.27), residues: 1047
  helix:  2.14 (0.24), residues: 472
  sheet: -1.60 (0.39), residues: 157
  loop : -0.63 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E1051 
 HIS   0.004   0.001   HIS E1262 
 PHE   0.011   0.001   PHE E 626 
 TYR   0.018   0.001   TYR E 475 
 ARG   0.005   0.000   ARG E  83 

*********************** 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
  151 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9214 (tpp) cc_final: 0.8711 (mpp)
REVERT: E   55 MET cc_start: 0.8402 (mmm) cc_final: 0.8072 (mmp)
REVERT: E   89 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7856 (p0)
REVERT: E  123 LEU cc_start: 0.8665 (mt) cc_final: 0.8448 (mp)
REVERT: E  254 MET cc_start: 0.7961 (mmt) cc_final: 0.7732 (mmt)
REVERT: E  475 TYR cc_start: 0.7026 (m-80) cc_final: 0.6763 (m-80)
REVERT: E  479 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8923 (mm)
REVERT: E  512 ASP cc_start: 0.7697 (t70) cc_final: 0.7381 (t70)
REVERT: E  646 MET cc_start: 0.7931 (mmm) cc_final: 0.7341 (mpp)
REVERT: E 1146 ILE cc_start: 0.8177 (mt) cc_final: 0.7690 (pt)
REVERT: E 1315 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.6557 (m90)
REVERT: E 1323 TYR cc_start: 0.7200 (m-10) cc_final: 0.6780 (m-10)
  outliers start: 34
  outliers final: 23
  residues processed: 138
  average time/residue: 0.1962
  time to fit residues: 38.7913
Evaluate side-chains
  137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  142 LYS
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  239 ASN
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  444 VAL
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  651 LEU
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  836 SER
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1088 THR
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1161 ILE
Chi-restraints excluded: chain E residue 1197 MET
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 1315 HIS
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:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0170
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0980
   chunk 79 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 77 optimal weight:    0.3980
   overall best weight:    0.3618

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

Flipped N/Q/H residues before XYZ refinement:
E 326 ASN
** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1315 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.161905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.138954 restraints weight = 11379.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.96
r_work: 0.3432 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2236

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= 0.220
  Angle     :  0.514   8.627  11787  Z= 0.264
  Chirality :  0.043   0.157   1332
  Planarity :  0.004   0.041   1503
  Dihedral  :  3.877  20.210   1146
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 15.26 %
    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:  0.69 (0.26), residues: 1047
  helix:  2.13 (0.24), residues: 472
  sheet: -1.55 (0.39), residues: 157
  loop : -0.64 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E1051 
 HIS   0.004   0.001   HIS E1262 
 PHE   0.014   0.001   PHE E 626 
 TYR   0.020   0.001   TYR E 475 
 ARG   0.005   0.000   ARG E  83 

*********************** 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
  153 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9295 (tpp) cc_final: 0.8779 (mpp)
REVERT: E   55 MET cc_start: 0.8423 (mmm) cc_final: 0.8104 (mmp)
REVERT: E   89 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7937 (p0)
REVERT: E  280 MET cc_start: 0.7976 (ttm) cc_final: 0.7603 (mtp)
REVERT: E  337 PHE cc_start: 0.8639 (m-80) cc_final: 0.8399 (m-80)
REVERT: E  479 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8823 (mm)
REVERT: E  512 ASP cc_start: 0.7794 (t70) cc_final: 0.7462 (t70)
REVERT: E  646 MET cc_start: 0.8006 (mmm) cc_final: 0.7391 (mpp)
REVERT: E  651 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9245 (tt)
REVERT: E 1146 ILE cc_start: 0.8207 (mt) cc_final: 0.7691 (pt)
REVERT: E 1315 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6545 (m90)
REVERT: E 1323 TYR cc_start: 0.7128 (m-10) cc_final: 0.6636 (m-10)
  outliers start: 38
  outliers final: 24
  residues processed: 138
  average time/residue: 0.1961
  time to fit residues: 38.2927
Evaluate side-chains
  138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  142 LYS
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  186 MET
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  444 VAL
Chi-restraints excluded: chain E residue  451 ASP
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  651 LEU
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  836 SER
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1156 MET
Chi-restraints excluded: chain E residue 1197 MET
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1315 HIS
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:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 85 optimal weight:    0.0570
   chunk 80 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 547 HIS
E 810 GLN
** E1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1315 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.158636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.135309 restraints weight = 11439.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.98
r_work: 0.3429 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2502

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= 0.282
  Angle     :  0.540   8.749  11787  Z= 0.277
  Chirality :  0.044   0.157   1332
  Planarity :  0.004   0.039   1503
  Dihedral  :  3.969  20.777   1146
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.58 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.80 %
    Favored  : 80.26 %
  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:  0.63 (0.26), residues: 1047
  helix:  2.01 (0.24), residues: 477
  sheet: -1.53 (0.39), residues: 162
  loop : -0.60 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1051 
 HIS   0.009   0.001   HIS E1315 
 PHE   0.014   0.001   PHE E 626 
 TYR   0.018   0.001   TYR E 475 
 ARG   0.006   0.000   ARG E  83 

*********************** 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
  161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9289 (tpp) cc_final: 0.8718 (mpp)
REVERT: E   55 MET cc_start: 0.8468 (mmm) cc_final: 0.8248 (mmp)
REVERT: E   89 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7962 (p0)
REVERT: E  142 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6576 (mttp)
REVERT: E  280 MET cc_start: 0.8114 (ttm) cc_final: 0.7797 (mtp)
REVERT: E  479 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8771 (mm)
REVERT: E  485 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7551 (tpp-160)
REVERT: E  512 ASP cc_start: 0.7817 (t70) cc_final: 0.7438 (t70)
REVERT: E 1172 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8360 (tp)
REVERT: E 1243 MET cc_start: 0.6952 (ttt) cc_final: 0.5856 (tpt)
REVERT: E 1323 TYR cc_start: 0.7137 (m-10) cc_final: 0.6701 (m-10)
  outliers start: 37
  outliers final: 26
  residues processed: 146
  average time/residue: 0.2105
  time to fit residues: 42.4038
Evaluate side-chains
  139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  142 LYS
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  836 SER
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1038 ILE
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1064 ASN
Chi-restraints excluded: chain E residue 1088 THR
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1156 MET
Chi-restraints excluded: chain E residue 1161 ILE
Chi-restraints excluded: chain E residue 1172 LEU
Chi-restraints excluded: chain E residue 1197 MET
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1210 HIS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.133019 restraints weight = 11545.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.96
r_work: 0.3402 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8666  Z= 0.336
  Angle     :  0.586   8.443  11787  Z= 0.300
  Chirality :  0.045   0.156   1332
  Planarity :  0.004   0.045   1503
  Dihedral  :  4.157  22.426   1146
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.68 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.44 %
    Favored  : 79.51 %
  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:  0.44 (0.27), residues: 1047
  helix:  1.88 (0.24), residues: 476
  sheet: -1.77 (0.37), residues: 173
  loop : -0.62 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E1051 
 HIS   0.005   0.001   HIS E1262 
 PHE   0.015   0.002   PHE E 626 
 TYR   0.019   0.002   TYR E 475 
 ARG   0.004   0.000   ARG E1000 

*********************** 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
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9266 (tpp) cc_final: 0.8629 (mpp)
REVERT: E   55 MET cc_start: 0.8447 (mmm) cc_final: 0.8229 (mmp)
REVERT: E   89 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7873 (p0)
REVERT: E   91 LEU cc_start: 0.8262 (mp) cc_final: 0.7977 (mp)
REVERT: E  378 MET cc_start: 0.8849 (mmm) cc_final: 0.8540 (mmm)
REVERT: E  479 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8812 (mm)
REVERT: E  512 ASP cc_start: 0.7809 (t70) cc_final: 0.7401 (t70)
REVERT: E  646 MET cc_start: 0.8115 (mmm) cc_final: 0.7420 (mpp)
REVERT: E 1113 GLN cc_start: 0.8298 (tt0) cc_final: 0.8017 (tt0)
REVERT: E 1172 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8540 (tp)
REVERT: E 1207 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6500 (p90)
  outliers start: 38
  outliers final: 27
  residues processed: 142
  average time/residue: 0.2006
  time to fit residues: 40.3293
Evaluate side-chains
  144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  239 ASN
Chi-restraints excluded: chain E residue  294 LEU
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  499 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  836 SER
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1038 ILE
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1064 ASN
Chi-restraints excluded: chain E residue 1088 THR
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1156 MET
Chi-restraints excluded: chain E residue 1161 ILE
Chi-restraints excluded: chain E residue 1172 LEU
Chi-restraints excluded: chain E residue 1197 MET
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1210 HIS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0470
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0970
   chunk 4 optimal weight:    0.0980
   chunk 28 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 629 ASN
** E1310 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 = 0.3808 r_free = 0.3808 target = 0.158125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.135795 restraints weight = 11561.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.85
r_work: 0.3411 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3065

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= 0.210
  Angle     :  0.526   7.663  11787  Z= 0.269
  Chirality :  0.043   0.183   1332
  Planarity :  0.004   0.042   1503
  Dihedral  :  4.056  20.963   1146
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.20 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.18 %
    Favored  : 79.08 %
  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:  0.54 (0.26), residues: 1047
  helix:  2.00 (0.24), residues: 474
  sheet: -1.65 (0.38), residues: 165
  loop : -0.68 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E1051 
 HIS   0.003   0.001   HIS E1210 
 PHE   0.011   0.001   PHE E 626 
 TYR   0.021   0.001   TYR E 475 
 ARG   0.003   0.000   ARG E1000 

*********************** 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
  162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9213 (tpp) cc_final: 0.8634 (mpp)
REVERT: E   89 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7829 (p0)
REVERT: E  378 MET cc_start: 0.8696 (mmm) cc_final: 0.8435 (mmm)
REVERT: E  422 MET cc_start: 0.8004 (mtt) cc_final: 0.7784 (mtp)
REVERT: E  479 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8839 (mm)
REVERT: E  512 ASP cc_start: 0.7760 (t70) cc_final: 0.7364 (t70)
REVERT: E  646 MET cc_start: 0.7970 (mmm) cc_final: 0.7323 (mpp)
REVERT: E 1113 GLN cc_start: 0.8088 (tt0) cc_final: 0.7877 (tt0)
REVERT: E 1207 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6594 (p90)
  outliers start: 35
  outliers final: 23
  residues processed: 149
  average time/residue: 0.2051
  time to fit residues: 43.2901
Evaluate side-chains
  141 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  196 CYS
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  386 VAL
Chi-restraints excluded: chain E residue  451 ASP
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  836 SER
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1088 THR
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1156 MET
Chi-restraints excluded: chain E residue 1197 MET
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1210 HIS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0770
   chunk 78 optimal weight:    0.0980
   chunk 99 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0010
   chunk 12 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.1322

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

Flipped N/Q/H residues before XYZ refinement:
E 183 GLN
** E1310 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 = 0.3835 r_free = 0.3835 target = 0.160589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138628 restraints weight = 11574.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.86
r_work: 0.3446 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8666  Z= 0.160
  Angle     :  0.514   8.348  11787  Z= 0.261
  Chirality :  0.042   0.151   1332
  Planarity :  0.004   0.040   1503
  Dihedral  :  3.928  18.584   1146
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.82 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.46 %
    Favored  : 78.34 %
  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:  0.57 (0.26), residues: 1047
  helix:  2.01 (0.24), residues: 476
  sheet: -1.43 (0.39), residues: 158
  loop : -0.79 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1051 
 HIS   0.003   0.000   HIS E1210 
 PHE   0.010   0.001   PHE E 337 
 TYR   0.018   0.001   TYR E 475 
 ARG   0.004   0.000   ARG E 213 

*********************** 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
  159 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9184 (tpp) cc_final: 0.8670 (mpp)
REVERT: E   89 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7688 (p0)
REVERT: E  168 ASN cc_start: 0.8049 (p0) cc_final: 0.7838 (p0)
REVERT: E  237 MET cc_start: 0.7151 (ptm) cc_final: 0.6902 (ttm)
REVERT: E  378 MET cc_start: 0.8648 (mmm) cc_final: 0.8377 (mmm)
REVERT: E  422 MET cc_start: 0.7966 (mtt) cc_final: 0.7748 (mtp)
REVERT: E  479 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8879 (mm)
REVERT: E  512 ASP cc_start: 0.7720 (t70) cc_final: 0.7306 (t70)
REVERT: E  646 MET cc_start: 0.7850 (mmm) cc_final: 0.7208 (mpp)
REVERT: E  817 HIS cc_start: 0.8309 (m-70) cc_final: 0.8102 (m170)
REVERT: E 1113 GLN cc_start: 0.8051 (tt0) cc_final: 0.7835 (tm-30)
REVERT: E 1207 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6684 (p90)
REVERT: E 1243 MET cc_start: 0.7133 (ttt) cc_final: 0.6170 (tpt)
  outliers start: 30
  outliers final: 25
  residues processed: 150
  average time/residue: 0.1974
  time to fit residues: 41.8274
Evaluate side-chains
  143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  196 CYS
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  451 ASP
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  499 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1088 THR
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1129 VAL
Chi-restraints excluded: chain E residue 1156 MET
Chi-restraints excluded: chain E residue 1197 MET
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1210 HIS
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1330 VAL
Chi-restraints excluded: chain G residue  406 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0870
   chunk 101 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135238 restraints weight = 11375.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.86
r_work: 0.3413 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8666  Z= 0.249
  Angle     :  0.549   7.966  11787  Z= 0.276
  Chirality :  0.044   0.187   1332
  Planarity :  0.004   0.042   1503
  Dihedral  :  3.979  22.368   1146
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.39 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.21 %
    Favored  : 77.91 %
  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:  0.53 (0.26), residues: 1047
  helix:  2.03 (0.24), residues: 474
  sheet: -1.45 (0.38), residues: 164
  loop : -0.84 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E1051 
 HIS   0.004   0.001   HIS E1262 
 PHE   0.014   0.002   PHE E 278 
 TYR   0.018   0.001   TYR E 475 
 ARG   0.009   0.000   ARG E 660 

********************** 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
  144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   31 MET cc_start: 0.9219 (tpp) cc_final: 0.8615 (mpp)
REVERT: E   89 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7762 (p0)
REVERT: E  237 MET cc_start: 0.7221 (ptm) cc_final: 0.6946 (ttm)
REVERT: E  378 MET cc_start: 0.8643 (mmm) cc_final: 0.8368 (mmm)
REVERT: E  422 MET cc_start: 0.7990 (mtt) cc_final: 0.7756 (mtp)
REVERT: E  479 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8910 (mm)
REVERT: E  512 ASP cc_start: 0.7831 (t70) cc_final: 0.7418 (t70)
REVERT: E  646 MET cc_start: 0.7958 (mmm) cc_final: 0.7274 (mpp)
REVERT: E 1113 GLN cc_start: 0.8253 (tt0) cc_final: 0.7988 (tt0)
REVERT: E 1207 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6833 (p90)
REVERT: E 1243 MET cc_start: 0.6937 (ttt) cc_final: 0.6083 (tpt)
  outliers start: 27
  outliers final: 22
  residues processed: 136
  average time/residue: 0.1981
  time to fit residues: 38.5008
Evaluate side-chains
  140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  196 CYS
Chi-restraints excluded: chain E residue  307 THR
Chi-restraints excluded: chain E residue  451 ASP
Chi-restraints excluded: chain E residue  479 LEU
Chi-restraints excluded: chain E residue  499 LEU
Chi-restraints excluded: chain E residue  503 SER
Chi-restraints excluded: chain E residue  584 ILE
Chi-restraints excluded: chain E residue  647 MET
Chi-restraints excluded: chain E residue  658 MET
Chi-restraints excluded: chain E residue  670 LEU
Chi-restraints excluded: chain E residue  969 GLN
Chi-restraints excluded: chain E residue 1011 THR
Chi-restraints excluded: chain E residue 1051 TRP
Chi-restraints excluded: chain E residue 1109 VAL
Chi-restraints excluded: chain E residue 1156 MET
Chi-restraints excluded: chain E residue 1197 MET
Chi-restraints excluded: chain E residue 1207 TYR
Chi-restraints excluded: chain E residue 1210 HIS
Chi-restraints excluded: chain E residue 1257 THR
Chi-restraints excluded: chain E residue 1259 LEU
Chi-restraints excluded: chain E residue 1330 VAL
Chi-restraints excluded: chain G residue  406 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0370
   chunk 88 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.4858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.133583 restraints weight = 11717.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.78
r_work: 0.3415 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8666  Z= 0.269
  Angle     :  0.559   8.097  11787  Z= 0.283
  Chirality :  0.044   0.172   1332
  Planarity :  0.004   0.043   1503
  Dihedral  :  4.084  24.784   1146
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.42 %
    Favored  : 77.69 %
  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:  0.54 (0.26), residues: 1047
  helix:  2.02 (0.24), residues: 474
  sheet: -1.50 (0.38), residues: 164
  loop : -0.79 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E1049 
 HIS   0.004   0.001   HIS E1262 
 PHE   0.012   0.002   PHE E 278 
 TYR   0.021   0.001   TYR E 475 
 ARG   0.006   0.000   ARG E 660 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4631.68 seconds
wall clock time: 83 minutes 46.41 seconds (5026.41 seconds total)