Starting phenix.real_space_refine
on Wed Sep 17 15:15:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b8r_44356/09_2025/9b8r_44356.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b8r_44356/09_2025/9b8r_44356.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b8r_44356/09_2025/9b8r_44356.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b8r_44356/09_2025/9b8r_44356.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b8r_44356/09_2025/9b8r_44356.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b8r_44356/09_2025/9b8r_44356.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.047
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      22      5.49       5
     S      47      5.16       5
     C    5939      2.51       5
     N    1590      2.21       5
     O    1823      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 103 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9425
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "P"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 202
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "T"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 248
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "E"
      Number of atoms: 8967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1119, 8967
          Classifications: {'peptide': 1119}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1066}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 162
          Unresolved non-hydrogen angles: 203
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 4, 'ASP:plan': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 96
    Chain: "E"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5209  SG  CYS E 665      45.858  64.745  17.877  1.00 81.51           S
  ATOM   5297  SG  CYS E 677      52.149  64.661  17.029  1.00 87.54           S
  ATOM   6033  SG  CYS E 763      51.160  66.480  22.121  1.00 94.87           S
  ATOM   5226  SG  CYS E 668      49.284  70.341  17.828  1.00 78.76           S

  Time building chain proxies: 2.36, per 1000 atoms: 0.25
  Number of scatterers: 9425
  At special positions: 0
  Unit cell: (100.188, 110.952, 106.812, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      47     16.00
     P      22     15.00
     O    1823      8.00
     N    1590      7.00
     C    5939      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: 1.05
  Conformation dependent library (CDL) restraints added in 378.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 E1401 "
        pdb="FE4  SF4 E1401 " - pdb=" SG  CYS E 668 "
        pdb="FE1  SF4 E1401 " - pdb=" SG  CYS E 665 "
        pdb="FE2  SF4 E1401 " - pdb=" SG  CYS E 677 "
        pdb="FE3  SF4 E1401 " - pdb=" SG  CYS E 763 "
      Number of angles added : 12


  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2130

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 13 sheets defined
      49.2% alpha, 17.6% beta
      5 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'E' and resid 27 through 50
    Processing helix  chain 'E' and resid 65 through 69
      removed outlier: 3.549A  pdb=" N   ILE E  69 " --> pdb=" O   ALA E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 145 through 147
      No H-bonds generated for 'chain 'E' and resid 145 through 147'
    Processing helix  chain 'E' and resid 148 through 160
    Processing helix  chain 'E' and resid 179 through 183
    Processing helix  chain 'E' and resid 195 through 216
      Proline residue:  E 208  - end of helix
    Processing helix  chain 'E' and resid 234 through 237
    Processing helix  chain 'E' and resid 248 through 257
    Processing helix  chain 'E' and resid 354 through 370
    Processing helix  chain 'E' and resid 382 through 394
    Processing helix  chain 'E' and resid 397 through 403
    Processing helix  chain 'E' and resid 422 through 429
    Processing helix  chain 'E' and resid 433 through 437
      removed outlier: 3.773A  pdb=" N   GLN E 437 " --> pdb=" O   GLN E 434 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 447
    Processing helix  chain 'E' and resid 455 through 466
      removed outlier: 4.670A  pdb=" N   THR E 460 " --> pdb=" O   PRO E 456 " (cutoff:3.500A)
      Proline residue:  E 461  - end of helix
      removed outlier: 4.164A  pdb=" N   PHE E 464 " --> pdb=" O   THR E 460 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 466 through 488
    Processing helix  chain 'E' and resid 488 through 498
      removed outlier: 3.517A  pdb=" N   PHE E 492 " --> pdb=" O   TYR E 488 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 503 through 510
    Processing helix  chain 'E' and resid 511 through 527
    Processing helix  chain 'E' and resid 577 through 598
      Proline residue:  E 589  - end of helix
    Processing helix  chain 'E' and resid 603 through 607
    Processing helix  chain 'E' and resid 609 through 627
    Processing helix  chain 'E' and resid 643 through 653
    Processing helix  chain 'E' and resid 661 through 668
    Processing helix  chain 'E' and resid 693 through 706
      removed outlier: 3.770A  pdb=" N   ASN E 706 " --> pdb=" O   ARG E 702 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 727 through 747
    Processing helix  chain 'E' and resid 769 through 798
      removed outlier: 3.974A  pdb=" N   ILE E 798 " --> pdb=" O   ASN E 794 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 806 through 834
      removed outlier: 3.523A  pdb=" N   LYS E 810 " --> pdb=" O   ARG E 806 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 843 through 869
      removed outlier: 3.633A  pdb=" N   ILE E 849 " --> pdb=" O   GLU E 845 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG E 867 " --> pdb=" O   ALA E 863 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 905 through 919
      removed outlier: 3.967A  pdb=" N   LEU E 910 " --> pdb=" O   PRO E 906 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG E 913 " --> pdb=" O   MET E 909 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR E 919 " --> pdb=" O   HIS E 915 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 993 through 1003
    Processing helix  chain 'E' and resid 1004 through 1008
    Processing helix  chain 'E' and resid 1011 through 1032
      removed outlier: 3.709A  pdb=" N   VAL E1022 " --> pdb=" O   ALA E1018 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1038 through 1047
    Processing helix  chain 'E' and resid 1055 through 1060
      removed outlier: 3.750A  pdb=" N   GLU E1060 " --> pdb=" O   LYS E1057 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1064 through 1078
    Processing helix  chain 'E' and resid 1079 through 1083
    Processing helix  chain 'E' and resid 1110 through 1114
    Processing helix  chain 'E' and resid 1115 through 1128
    Processing helix  chain 'E' and resid 1136 through 1141
    Processing helix  chain 'E' and resid 1142 through 1158
    Processing helix  chain 'E' and resid 1158 through 1165
    Processing helix  chain 'E' and resid 1177 through 1184
    Processing sheet with id=AA1, first strand: chain 'E' and resid 75 through 78
      removed outlier: 3.746A  pdb=" N   ARG E  75 " --> pdb=" O   VAL E 267 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   TRP E 264 " --> pdb=" O   ASP E 275 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 81 through 87
      removed outlier: 3.525A  pdb=" N   PHE E 129 " --> pdb=" O   PHE E 121 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 166 through 172
      removed outlier: 6.889A  pdb=" N   THR E 187 " --> pdb=" O   CYS E 143 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   CYS E 143 " --> pdb=" O   THR E 187 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP E 241 " --> pdb=" O   ALA E 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 335 through 336
      removed outlier: 6.869A  pdb=" N   GLY E 319 " --> pdb=" O   THR E 348 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   PHE E 350 " --> pdb=" O   GLY E 319 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU E 321 " --> pdb=" O   PHE E 350 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   GLU E 352 " --> pdb=" O   LEU E 321 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   THR E 323 " --> pdb=" O   GLU E 352 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   MET E 309 " --> pdb=" O   ASN E 324 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLU E 292 " --> pdb=" O   MET E 309 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   ILE E 311 " --> pdb=" O   ASP E 290 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ASP E 290 " --> pdb=" O   ILE E 311 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   TYR E 313 " --> pdb=" O   ALA E 288 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA E 288 " --> pdb=" O   TYR E 313 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE E 315 " --> pdb=" O   VAL E 286 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL E 286 " --> pdb=" O   ILE E 315 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   MET E 287 " --> pdb=" O   SER E 375 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ILE E 374 " --> pdb=" O   MET E 420 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 405 through 406
    Processing sheet with id=AA6, first strand: chain 'E' and resid 542 through 543
    Processing sheet with id=AA7, first strand: chain 'E' and resid 558 through 560
      removed outlier: 6.926A  pdb=" N   TRP E 880 " --> pdb=" O   LEU E 872 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LEU E 874 " --> pdb=" O   GLY E 878 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLY E 878 " --> pdb=" O   LEU E 874 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ILE E 636 " --> pdb=" O   PRO E 949 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 564 through 567
    Processing sheet with id=AA9, first strand: chain 'E' and resid 572 through 575
    Processing sheet with id=AB1, first strand: chain 'E' and resid 708 through 710
    Processing sheet with id=AB2, first strand: chain 'E' and resid 890 through 894
    Processing sheet with id=AB3, first strand: chain 'E' and resid 920 through 928
      removed outlier: 4.044A  pdb=" N   GLN E 922 " --> pdb=" O   HIS E 937 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   HIS E 937 " --> pdb=" O   GLN E 922 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLN E 924 " --> pdb=" O   GLU E 935 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLU E 935 " --> pdb=" O   GLN E 924 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   LEU E 926 " --> pdb=" O   ILE E 933 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ILE E 933 " --> pdb=" O   LEU E 926 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 991 through 992
      removed outlier: 4.049A  pdb=" N   ASN E1049 " --> pdb=" O   GLU E 991 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1329 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      12 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 2.12

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.18 -     1.40: 3464
        1.40 -     1.62: 6138
        1.62 -     1.83: 72
        1.83 -     2.05: 0
        2.05 -     2.27: 12
  Bond restraints: 9686
  Sorted by residual:
  bond pdb=" C   PRO E 949 "
       pdb=" N   TYR E 950 "
    ideal  model  delta    sigma   weight residual
    1.331  1.563 -0.232 1.30e-02 5.92e+03 3.18e+02
  bond pdb=" C   GLU E 766 "
       pdb=" N   ASN E 767 "
    ideal  model  delta    sigma   weight residual
    1.331  1.555 -0.224 2.07e-02 2.33e+03 1.18e+02
  bond pdb=" N   ILE E1107 "
       pdb=" CA  ILE E1107 "
    ideal  model  delta    sigma   weight residual
    1.462  1.403  0.059 1.01e-02 9.80e+03 3.36e+01
  bond pdb=" C   ASN E1169 "
       pdb=" N   PRO E1170 "
    ideal  model  delta    sigma   weight residual
    1.337  1.397 -0.061 1.11e-02 8.12e+03 2.99e+01
  bond pdb=" C1'  DG P   3 "
       pdb=" N9   DG P   3 "
    ideal  model  delta    sigma   weight residual
    1.460  1.352  0.108 2.00e-02 2.50e+03 2.92e+01
  ... (remaining 9681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 11829
        2.81 -     5.62: 1284
        5.62 -     8.43: 71
        8.43 -    11.24: 13
       11.24 -    14.04: 5
  Bond angle restraints: 13202
  Sorted by residual:
  angle pdb=" O   GLU E 766 "
        pdb=" C   GLU E 766 "
        pdb=" N   ASN E 767 "
      ideal   model   delta    sigma   weight residual
     122.95  111.71   11.24 1.24e+00 6.50e-01 8.21e+01
  angle pdb=" N   LEU E 122 "
        pdb=" CA  LEU E 122 "
        pdb=" C   LEU E 122 "
      ideal   model   delta    sigma   weight residual
     111.75  100.75   11.00 1.28e+00 6.10e-01 7.38e+01
  angle pdb=" N   PRO E 656 "
        pdb=" CA  PRO E 656 "
        pdb=" C   PRO E 656 "
      ideal   model   delta    sigma   weight residual
     114.98  103.71   11.27 1.46e+00 4.69e-01 5.96e+01
  angle pdb=" CA  ASP E 151 "
        pdb=" CB  ASP E 151 "
        pdb=" CG  ASP E 151 "
      ideal   model   delta    sigma   weight residual
     112.60  120.19   -7.59 1.00e+00 1.00e+00 5.76e+01
  angle pdb=" C   LYS E 751 "
        pdb=" CA  LYS E 751 "
        pdb=" CB  LYS E 751 "
      ideal   model   delta    sigma   weight residual
     112.09  102.10    9.99 1.43e+00 4.89e-01 4.88e+01
  ... (remaining 13197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 5142
       16.90 -    33.81: 450
       33.81 -    50.71: 136
       50.71 -    67.62: 54
       67.62 -    84.52: 10
  Dihedral angle restraints: 5792
    sinusoidal: 2496
      harmonic: 3296
  Sorted by residual:
  dihedral pdb=" CA  ARG E 749 "
           pdb=" C   ARG E 749 "
           pdb=" N   VAL E 750 "
           pdb=" CA  VAL E 750 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.78  -40.22     0      5.00e+00 4.00e-02 6.47e+01
  dihedral pdb=" CA  ARG E 672 "
           pdb=" C   ARG E 672 "
           pdb=" N   PRO E 673 "
           pdb=" CA  PRO E 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.90   27.10     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  PRO E 634 "
           pdb=" C   PRO E 634 "
           pdb=" N   LEU E 635 "
           pdb=" CA  LEU E 635 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.41   25.59     0      5.00e+00 4.00e-02 2.62e+01
  ... (remaining 5789 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1182
       0.125 -    0.249: 219
       0.249 -    0.374: 29
       0.374 -    0.499: 4
       0.499 -    0.624: 7
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" P    DC P   1 "
            pdb=" OP1  DC P   1 "
            pdb=" OP2  DC P   1 "
            pdb=" O5'  DC P   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.72e+00
  chirality pdb=" P    DT T   3 "
            pdb=" OP1  DT T   3 "
            pdb=" OP2  DT T   3 "
            pdb=" O5'  DT T   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.61 2.00e-01 2.50e+01 9.23e+00
  chirality pdb=" P    DG P   6 "
            pdb=" OP1  DG P   6 "
            pdb=" OP2  DG P   6 "
            pdb=" O5'  DG P   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.93   -0.58 2.00e-01 2.50e+01 8.54e+00
  ... (remaining 1438 not shown)

  Planarity restraints: 1628
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E  81 "   -0.052 2.00e-02 2.50e+03   1.03e-01 1.07e+02
        pdb=" C   ASN E  81 "    0.179 2.00e-02 2.50e+03
        pdb=" O   ASN E  81 "   -0.070 2.00e-02 2.50e+03
        pdb=" N   MET E  82 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO E 949 "   -0.046 2.00e-02 2.50e+03   9.21e-02 8.49e+01
        pdb=" C   PRO E 949 "    0.159 2.00e-02 2.50e+03
        pdb=" O   PRO E 949 "   -0.067 2.00e-02 2.50e+03
        pdb=" N   TYR E 950 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 485 "   -0.119 2.00e-02 2.50e+03   6.35e-02 8.07e+01
        pdb=" CG  TYR E 485 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 485 "    0.070 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 485 "    0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 485 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 485 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 485 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E 485 "   -0.087 2.00e-02 2.50e+03
  ... (remaining 1625 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 572
        2.74 -     3.28: 9248
        3.28 -     3.82: 15270
        3.82 -     4.36: 20063
        4.36 -     4.90: 31911
  Nonbonded interactions: 77064
  Sorted by model distance:
  nonbonded pdb=" O   GLU E 845 "
            pdb=" N   ALA E 847 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   LEU E 815 "
            pdb=" OG  SER E 818 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   GLU E 845 "
            pdb=" N   GLY E 848 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" N   ARG E 260 "
            pdb=" OH  TYR E 265 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   GLU E 124 "
            pdb=" N   GLY E 126 "
     model   vdw
     2.296 3.120
  ... (remaining 77059 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.170
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5517
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      :  0.016   0.534   9690  Z= 0.909
  Angle     :  1.856  38.405  13214  Z= 1.157
  Chirality :  0.106   0.624   1441
  Planarity :  0.016   0.177   1628
  Dihedral  : 15.435  84.520   3662
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  4.31 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  4.42 %
    Favored  : 93.52 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.23), residues: 1113
  helix: -0.90 (0.21), residues: 459
  sheet: -0.93 (0.35), residues: 197
  loop : -1.29 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG E 781 
 TYR   0.119   0.018   TYR E 485 
 PHE   0.071   0.010   PHE E 347 
 TRP   0.106   0.016   TRP E 384 
 HIS   0.021   0.005   HIS E 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.01452 ( 9686)
  covalent geometry    : angle       1.75393 (13202)
  hydrogen bonds       : bond        0.18761 (  488)
  hydrogen bonds       : angle       7.33997 ( 1353)
  metal coordination   : bond        0.32326 (    4)
  metal coordination   : angle      20.24678 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 300
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4688 (t80)
REVERT: E   86 LEU cc_start: 0.8801 (tp) cc_final: 0.8513 (mp)
REVERT: E  242 ILE cc_start: 0.8427 (pt) cc_final: 0.8189 (mt)
REVERT: E  265 TYR cc_start: 0.6297 (m-80) cc_final: 0.5525 (m-80)
REVERT: E  604 VAL cc_start: 0.6580 (m) cc_final: 0.6207 (m)
REVERT: E  645 TYR cc_start: 0.7523 (m-10) cc_final: 0.7167 (m-10)
REVERT: E  926 LEU cc_start: 0.6822 (tt) cc_final: 0.6605 (tp)
  outliers start: 20
  outliers final: 3
  residues processed: 313
  average time/residue: 0.1300
  time to fit residues: 53.2544
Evaluate side-chains
  160 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 156
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue  689 PHE
Chi-restraints excluded: chain E residue  827 LEU
Chi-restraints excluded: chain E residue 1038 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.0010
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
E 572 ASN
E 794 ASN
E 823 HIS
E1062 GLN
E1176 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.165804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.134246 restraints weight = 19940.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.137862 restraints weight = 9886.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.140140 restraints weight = 6425.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.141630 restraints weight = 4981.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.142408 restraints weight = 4282.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9690  Z= 0.168
  Angle     :  0.810  37.219  13214  Z= 0.369
  Chirality :  0.045   0.236   1441
  Planarity :  0.005   0.064   1628
  Dihedral  : 13.684  77.063   1463
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.70 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.27 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.25), residues: 1113
  helix:  1.07 (0.24), residues: 473
  sheet: -0.24 (0.35), residues: 194
  loop : -0.40 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 988 
 TYR   0.016   0.002   TYR E 770 
 PHE   0.026   0.002   PHE E 381 
 TRP   0.017   0.002   TRP E1143 
 HIS   0.003   0.001   HIS E 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9686)
  covalent geometry    : angle       0.68319 (13202)
  hydrogen bonds       : bond        0.05246 (  488)
  hydrogen bonds       : angle       5.55771 ( 1353)
  metal coordination   : bond        0.01238 (    4)
  metal coordination   : angle      14.48573 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.5121 (t80)
REVERT: E  265 TYR cc_start: 0.6759 (m-80) cc_final: 0.6210 (m-80)
REVERT: E  834 VAL cc_start: 0.8411 (p) cc_final: 0.8084 (p)
REVERT: E  957 SER cc_start: 0.7849 (t) cc_final: 0.7591 (p)
REVERT: E  992 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5339 (tt)
  outliers start: 27
  outliers final: 16
  residues processed: 183
  average time/residue: 0.1057
  time to fit residues: 26.9146
Evaluate side-chains
  136 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  246 ASP
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  413 LYS
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  474 SER
Chi-restraints excluded: chain E residue  572 ASN
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue  992 LEU
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1095 SER
Chi-restraints excluded: chain E residue 1154 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 88 optimal weight:    0.2980
   chunk 78 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
E  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.162022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.131895 restraints weight = 19919.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.133977 restraints weight = 10106.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.135405 restraints weight = 7219.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.135592 restraints weight = 5882.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.135871 restraints weight = 5450.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9690  Z= 0.146
  Angle     :  0.721  33.029  13214  Z= 0.330
  Chirality :  0.043   0.160   1441
  Planarity :  0.005   0.080   1628
  Dihedral  : 13.236  66.709   1456
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.98 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.81 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.26), residues: 1113
  helix:  1.36 (0.24), residues: 471
  sheet: -0.12 (0.35), residues: 200
  loop : -0.04 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E1138 
 TYR   0.012   0.001   TYR E 485 
 PHE   0.022   0.002   PHE E 984 
 TRP   0.011   0.001   TRP E 683 
 HIS   0.003   0.001   HIS E 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9686)
  covalent geometry    : angle       0.61640 (13202)
  hydrogen bonds       : bond        0.04625 (  488)
  hydrogen bonds       : angle       5.29489 ( 1353)
  metal coordination   : bond        0.00868 (    4)
  metal coordination   : angle      12.43184 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5466 (OUTLIER) cc_final: 0.5159 (t80)
REVERT: E  265 TYR cc_start: 0.7187 (m-80) cc_final: 0.6597 (m-80)
REVERT: E  557 HIS cc_start: 0.7488 (t70) cc_final: 0.6889 (t70)
REVERT: E  613 ILE cc_start: 0.7916 (mm) cc_final: 0.7506 (mt)
REVERT: E  957 SER cc_start: 0.7959 (t) cc_final: 0.7639 (p)
REVERT: E  968 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7835 (mtp85)
REVERT: E 1087 LEU cc_start: 0.4527 (tt) cc_final: 0.4042 (mt)
  outliers start: 27
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0969
  time to fit residues: 21.2525
Evaluate side-chains
  131 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  246 ASP
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  397 ASP
Chi-restraints excluded: chain E residue  413 LYS
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  474 SER
Chi-restraints excluded: chain E residue  497 CYS
Chi-restraints excluded: chain E residue  561 LEU
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue 1092 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 83 optimal weight:    0.6980
   chunk 75 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
E  29 ASN
E 924 GLN
E1176 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.152248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.122173 restraints weight = 20294.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.123860 restraints weight = 10295.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.126441 restraints weight = 7025.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.125830 restraints weight = 5628.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.126095 restraints weight = 5515.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.5535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9690  Z= 0.214
  Angle     :  0.779  31.203  13214  Z= 0.366
  Chirality :  0.046   0.172   1441
  Planarity :  0.005   0.095   1628
  Dihedral  : 13.328  69.613   1456
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.36 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.25), residues: 1113
  helix:  1.13 (0.24), residues: 482
  sheet: -0.10 (0.35), residues: 197
  loop : -0.10 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 370 
 TYR   0.022   0.002   TYR E 833 
 PHE   0.019   0.002   PHE E1122 
 TRP   0.012   0.002   TRP E 683 
 HIS   0.008   0.002   HIS E 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 9686)
  covalent geometry    : angle       0.68915 (13202)
  hydrogen bonds       : bond        0.04952 (  488)
  hydrogen bonds       : angle       5.26533 ( 1353)
  metal coordination   : bond        0.01568 (    4)
  metal coordination   : angle      12.06881 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.5320 (t80)
REVERT: E  207 ARG cc_start: 0.7515 (ppt170) cc_final: 0.7182 (ptt180)
REVERT: E  381 PHE cc_start: 0.7534 (t80) cc_final: 0.7294 (t80)
REVERT: E  904 SER cc_start: 0.8608 (t) cc_final: 0.8269 (p)
REVERT: E  957 SER cc_start: 0.8301 (t) cc_final: 0.7977 (p)
REVERT: E 1042 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7994 (tt)
REVERT: E 1052 MET cc_start: 0.5979 (mtp) cc_final: 0.5614 (mtm)
REVERT: E 1081 MET cc_start: 0.8010 (mmt) cc_final: 0.7685 (mmm)
REVERT: E 1087 LEU cc_start: 0.4801 (tt) cc_final: 0.4073 (mt)
REVERT: E 1091 TYR cc_start: 0.6594 (p90) cc_final: 0.6258 (p90)
  outliers start: 35
  outliers final: 22
  residues processed: 154
  average time/residue: 0.0933
  time to fit residues: 20.5817
Evaluate side-chains
  131 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  366 ILE
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  397 ASP
Chi-restraints excluded: chain E residue  413 LYS
Chi-restraints excluded: chain E residue  417 CYS
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  470 LEU
Chi-restraints excluded: chain E residue  497 CYS
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  699 MET
Chi-restraints excluded: chain E residue  771 VAL
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  879 ILE
Chi-restraints excluded: chain E residue 1042 LEU
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 102 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.150749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.120491 restraints weight = 20186.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.123110 restraints weight = 10177.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.124091 restraints weight = 7022.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.124247 restraints weight = 5858.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.124545 restraints weight = 5428.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.5978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9690  Z= 0.190
  Angle     :  0.725  29.120  13214  Z= 0.336
  Chirality :  0.044   0.173   1441
  Planarity :  0.004   0.082   1628
  Dihedral  : 13.245  67.229   1456
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.83 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.25), residues: 1113
  helix:  1.30 (0.24), residues: 478
  sheet: -0.12 (0.36), residues: 193
  loop : -0.10 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 988 
 TYR   0.013   0.002   TYR E 449 
 PHE   0.016   0.002   PHE E 984 
 TRP   0.016   0.002   TRP E1026 
 HIS   0.004   0.001   HIS E 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 9686)
  covalent geometry    : angle       0.63690 (13202)
  hydrogen bonds       : bond        0.04706 (  488)
  hydrogen bonds       : angle       5.26414 ( 1353)
  metal coordination   : bond        0.01169 (    4)
  metal coordination   : angle      11.54546 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.5367 (t80)
REVERT: E  904 SER cc_start: 0.8702 (t) cc_final: 0.8295 (p)
REVERT: E  957 SER cc_start: 0.8456 (t) cc_final: 0.8124 (p)
REVERT: E 1081 MET cc_start: 0.8034 (mmt) cc_final: 0.7657 (mmm)
REVERT: E 1087 LEU cc_start: 0.4633 (tt) cc_final: 0.4114 (mt)
REVERT: E 1091 TYR cc_start: 0.6524 (p90) cc_final: 0.6201 (p90)
REVERT: E 1164 LEU cc_start: 0.8477 (pp) cc_final: 0.8011 (mt)
  outliers start: 30
  outliers final: 22
  residues processed: 144
  average time/residue: 0.0960
  time to fit residues: 19.7049
Evaluate side-chains
  128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  267 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  397 ASP
Chi-restraints excluded: chain E residue  417 CYS
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  470 LEU
Chi-restraints excluded: chain E residue  497 CYS
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  771 VAL
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  879 ILE
Chi-restraints excluded: chain E residue  954 ILE
Chi-restraints excluded: chain E residue 1029 VAL
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0060
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
E 794 ASN
E 924 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.153920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.124265 restraints weight = 20215.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.126737 restraints weight = 10104.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.127587 restraints weight = 7112.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.127769 restraints weight = 6008.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.128029 restraints weight = 5484.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.6133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9690  Z= 0.120
  Angle     :  0.659  24.509  13214  Z= 0.305
  Chirality :  0.042   0.161   1441
  Planarity :  0.004   0.087   1628
  Dihedral  : 13.139  71.374   1456
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.14 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.26), residues: 1113
  helix:  1.59 (0.24), residues: 476
  sheet:  0.07 (0.36), residues: 194
  loop :  0.02 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 988 
 TYR   0.025   0.002   TYR E 449 
 PHE   0.019   0.001   PHE E 984 
 TRP   0.014   0.001   TRP E 841 
 HIS   0.002   0.001   HIS E 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9686)
  covalent geometry    : angle       0.58070 (13202)
  hydrogen bonds       : bond        0.03992 (  488)
  hydrogen bonds       : angle       5.07198 ( 1353)
  metal coordination   : bond        0.00470 (    4)
  metal coordination   : angle      10.32527 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.5276 (t80)
REVERT: E  644 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7371 (ttm)
REVERT: E  904 SER cc_start: 0.8640 (t) cc_final: 0.8409 (p)
REVERT: E  957 SER cc_start: 0.8403 (t) cc_final: 0.8089 (p)
REVERT: E 1081 MET cc_start: 0.8036 (mmt) cc_final: 0.7723 (mtp)
REVERT: E 1091 TYR cc_start: 0.6446 (p90) cc_final: 0.6172 (p90)
REVERT: E 1164 LEU cc_start: 0.8438 (pp) cc_final: 0.7937 (mt)
  outliers start: 25
  outliers final: 17
  residues processed: 138
  average time/residue: 0.0936
  time to fit residues: 18.4501
Evaluate side-chains
  124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  212 ASP
Chi-restraints excluded: chain E residue  267 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  470 LEU
Chi-restraints excluded: chain E residue  497 CYS
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  644 MET
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  919 THR
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1154 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.150559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.120894 restraints weight = 20391.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.122573 restraints weight = 10350.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.125749 restraints weight = 7100.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.125245 restraints weight = 5468.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.125377 restraints weight = 5004.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.6478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9690  Z= 0.167
  Angle     :  0.713  26.772  13214  Z= 0.330
  Chirality :  0.044   0.170   1441
  Planarity :  0.004   0.085   1628
  Dihedral  : 13.148  73.080   1456
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 19.34 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.26), residues: 1113
  helix:  1.51 (0.24), residues: 477
  sheet: -0.05 (0.36), residues: 194
  loop : -0.04 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 968 
 TYR   0.022   0.002   TYR E 449 
 PHE   0.015   0.002   PHE E1122 
 TRP   0.010   0.001   TRP E1143 
 HIS   0.005   0.001   HIS E 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 9686)
  covalent geometry    : angle       0.63820 (13202)
  hydrogen bonds       : bond        0.04510 (  488)
  hydrogen bonds       : angle       5.11133 ( 1353)
  metal coordination   : bond        0.01006 (    4)
  metal coordination   : angle      10.57428 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5631 (OUTLIER) cc_final: 0.5286 (t80)
REVERT: E  846 MET cc_start: 0.8032 (tmm) cc_final: 0.7743 (ppp)
REVERT: E  957 SER cc_start: 0.8470 (t) cc_final: 0.8105 (p)
REVERT: E 1081 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7597 (mtp)
REVERT: E 1087 LEU cc_start: 0.4527 (OUTLIER) cc_final: 0.4127 (mt)
REVERT: E 1091 TYR cc_start: 0.6655 (p90) cc_final: 0.6394 (p90)
  outliers start: 34
  outliers final: 25
  residues processed: 137
  average time/residue: 0.0975
  time to fit residues: 19.0697
Evaluate side-chains
  130 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  212 ASP
Chi-restraints excluded: chain E residue  267 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  309 MET
Chi-restraints excluded: chain E residue  366 ILE
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  470 LEU
Chi-restraints excluded: chain E residue  474 SER
Chi-restraints excluded: chain E residue  497 CYS
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  561 LEU
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  808 GLU
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue 1081 MET
Chi-restraints excluded: chain E residue 1087 LEU
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1095 SER
Chi-restraints excluded: chain E residue 1154 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0980
   chunk 78 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0010
   chunk 81 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.9990

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.151917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.122143 restraints weight = 20357.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.124280 restraints weight = 10949.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.125211 restraints weight = 7200.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.125718 restraints weight = 6587.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.125655 restraints weight = 5756.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.6626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9690  Z= 0.127
  Angle     :  0.684  24.114  13214  Z= 0.314
  Chirality :  0.042   0.171   1441
  Planarity :  0.004   0.090   1628
  Dihedral  : 13.073  73.146   1456
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.58 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1113
  helix:  1.63 (0.24), residues: 477
  sheet:  0.07 (0.36), residues: 201
  loop :  0.08 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 806 
 TYR   0.022   0.001   TYR E 449 
 PHE   0.011   0.001   PHE E 139 
 TRP   0.012   0.001   TRP E 841 
 HIS   0.002   0.001   HIS E 804 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9686)
  covalent geometry    : angle       0.61499 (13202)
  hydrogen bonds       : bond        0.04084 (  488)
  hydrogen bonds       : angle       5.01454 ( 1353)
  metal coordination   : bond        0.00504 (    4)
  metal coordination   : angle       9.91918 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.5213 (t80)
REVERT: E  644 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7215 (ttm)
REVERT: E  846 MET cc_start: 0.8186 (tmm) cc_final: 0.7894 (ppp)
REVERT: E  957 SER cc_start: 0.8461 (t) cc_final: 0.8079 (p)
REVERT: E 1081 MET cc_start: 0.8001 (mmt) cc_final: 0.7632 (mtp)
REVERT: E 1091 TYR cc_start: 0.6502 (p90) cc_final: 0.6260 (p90)
REVERT: E 1164 LEU cc_start: 0.8479 (pp) cc_final: 0.8047 (mt)
  outliers start: 27
  outliers final: 21
  residues processed: 132
  average time/residue: 0.0959
  time to fit residues: 18.2597
Evaluate side-chains
  125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  212 ASP
Chi-restraints excluded: chain E residue  267 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  309 MET
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  470 LEU
Chi-restraints excluded: chain E residue  474 SER
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  544 ASP
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  644 MET
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1095 SER
Chi-restraints excluded: chain E residue 1154 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 94 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0870
   chunk 76 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.5760

-------------------------------------------------------------------------------
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 = 0.4175 r_free = 0.4175 target = 0.153142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.123250 restraints weight = 20447.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.125826 restraints weight = 11071.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.126300 restraints weight = 7051.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.126699 restraints weight = 6482.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.127051 restraints weight = 5905.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.6758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9690  Z= 0.118
  Angle     :  0.669  22.124  13214  Z= 0.310
  Chirality :  0.042   0.166   1441
  Planarity :  0.004   0.086   1628
  Dihedral  : 13.033  75.631   1456
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.50 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.26), residues: 1113
  helix:  1.68 (0.24), residues: 475
  sheet:  0.13 (0.37), residues: 201
  loop :  0.04 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 806 
 TYR   0.019   0.001   TYR E 842 
 PHE   0.011   0.001   PHE E 784 
 TRP   0.013   0.001   TRP E 841 
 HIS   0.003   0.001   HIS E 804 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9686)
  covalent geometry    : angle       0.60700 (13202)
  hydrogen bonds       : bond        0.03945 (  488)
  hydrogen bonds       : angle       4.92440 ( 1353)
  metal coordination   : bond        0.00351 (    4)
  metal coordination   : angle       9.37115 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5584 (OUTLIER) cc_final: 0.5226 (t80)
REVERT: E  846 MET cc_start: 0.7975 (tmm) cc_final: 0.7692 (ppp)
REVERT: E  957 SER cc_start: 0.8474 (t) cc_final: 0.8113 (p)
REVERT: E 1036 MET cc_start: 0.7231 (mmm) cc_final: 0.6512 (mmp)
REVERT: E 1081 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7635 (mtp)
REVERT: E 1091 TYR cc_start: 0.6483 (p90) cc_final: 0.6267 (p90)
REVERT: E 1164 LEU cc_start: 0.8456 (pp) cc_final: 0.7962 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 130
  average time/residue: 0.0886
  time to fit residues: 17.1280
Evaluate side-chains
  127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  212 ASP
Chi-restraints excluded: chain E residue  267 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  309 MET
Chi-restraints excluded: chain E residue  369 VAL
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  470 LEU
Chi-restraints excluded: chain E residue  474 SER
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  544 ASP
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue 1081 MET
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1095 SER
Chi-restraints excluded: chain E residue 1154 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0030
   chunk 32 optimal weight:    0.0270
   chunk 92 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 95 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   overall best weight:    0.7250

-------------------------------------------------------------------------------
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 = 0.4177 r_free = 0.4177 target = 0.153175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.122137 restraints weight = 20372.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.125254 restraints weight = 10223.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.127254 restraints weight = 6741.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.128386 restraints weight = 5314.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.129105 restraints weight = 4666.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.6905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9690  Z= 0.118
  Angle     :  0.664  21.780  13214  Z= 0.308
  Chirality :  0.042   0.166   1441
  Planarity :  0.004   0.081   1628
  Dihedral  : 13.068  76.622   1456
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.91 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.26), residues: 1113
  helix:  1.69 (0.24), residues: 476
  sheet:  0.12 (0.37), residues: 203
  loop :  0.05 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 806 
 TYR   0.019   0.001   TYR E 842 
 PHE   0.013   0.001   PHE E 193 
 TRP   0.037   0.002   TRP E 791 
 HIS   0.002   0.000   HIS E 921 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9686)
  covalent geometry    : angle       0.60432 (13202)
  hydrogen bonds       : bond        0.03856 (  488)
  hydrogen bonds       : angle       4.85503 ( 1353)
  metal coordination   : bond        0.00402 (    4)
  metal coordination   : angle       9.17082 (   12)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   30 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.5325 (t80)
REVERT: E  846 MET cc_start: 0.8010 (tmm) cc_final: 0.7741 (ppp)
REVERT: E  957 SER cc_start: 0.8477 (t) cc_final: 0.8146 (p)
REVERT: E 1036 MET cc_start: 0.7180 (mmm) cc_final: 0.6491 (mmp)
REVERT: E 1081 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7718 (mtp)
REVERT: E 1087 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4413 (mt)
REVERT: E 1164 LEU cc_start: 0.8462 (pp) cc_final: 0.7935 (mt)
  outliers start: 25
  outliers final: 18
  residues processed: 127
  average time/residue: 0.0890
  time to fit residues: 16.5437
Evaluate side-chains
  125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue  191 LEU
Chi-restraints excluded: chain E residue  212 ASP
Chi-restraints excluded: chain E residue  267 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  305 VAL
Chi-restraints excluded: chain E residue  309 MET
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  474 SER
Chi-restraints excluded: chain E residue  497 CYS
Chi-restraints excluded: chain E residue  519 LEU
Chi-restraints excluded: chain E residue  544 ASP
Chi-restraints excluded: chain E residue  819 LEU
Chi-restraints excluded: chain E residue  941 THR
Chi-restraints excluded: chain E residue 1081 MET
Chi-restraints excluded: chain E residue 1087 LEU
Chi-restraints excluded: chain E residue 1092 ILE
Chi-restraints excluded: chain E residue 1095 SER
Chi-restraints excluded: chain E residue 1154 ILE
Chi-restraints excluded: chain E residue 1186 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 104 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.4128 r_free = 0.4128 target = 0.149364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117641 restraints weight = 20215.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.120699 restraints weight = 10127.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.122622 restraints weight = 6725.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.123613 restraints weight = 5343.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.124307 restraints weight = 4745.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.7124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9690  Z= 0.178
  Angle     :  0.708  26.323  13214  Z= 0.329
  Chirality :  0.044   0.170   1441
  Planarity :  0.004   0.088   1628
  Dihedral  : 13.143  73.728   1456
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 21.81 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1113
  helix:  1.51 (0.24), residues: 477
  sheet:  0.04 (0.37), residues: 197
  loop :  0.03 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 968 
 TYR   0.020   0.002   TYR E 449 
 PHE   0.022   0.002   PHE E 193 
 TRP   0.045   0.002   TRP E 791 
 HIS   0.005   0.001   HIS E 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9686)
  covalent geometry    : angle       0.63811 (13202)
  hydrogen bonds       : bond        0.04413 (  488)
  hydrogen bonds       : angle       4.96579 ( 1353)
  metal coordination   : bond        0.01029 (    4)
  metal coordination   : angle      10.16117 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1777.87 seconds
wall clock time: 31 minutes 24.44 seconds (1884.44 seconds total)