Starting phenix.real_space_refine
on Thu Feb 13 13:07:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yo3_33980/02_2025/7yo3_33980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yo3_33980/02_2025/7yo3_33980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yo3_33980/02_2025/7yo3_33980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yo3_33980/02_2025/7yo3_33980.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yo3_33980/02_2025/7yo3_33980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yo3_33980/02_2025/7yo3_33980.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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
     Ca      2      9.91       5
     Mg      1      5.21       5
     S      57      5.16       5
     C    5790      2.51       5
     N    1510      2.21       5
     O    1601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8961
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 882, 7034
          Classifications: {'peptide': 882}
          Link IDs: {'PTRANS': 27, 'TRANS': 854}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 1924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 1924
          Classifications: {'peptide': 262}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 239}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.50, per 1000 atoms: 0.61
  Number of scatterers: 8961
  At special positions: 0
  Unit cell: (127.488, 122.508, 176.292, 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)
     Ca      2     19.99
     S      57     16.00
     Mg      1     11.99
     O    1601      8.00
     N    1510      7.00
     C    5790      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  43 " - pdb=" SG  CYS B  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  47 " - pdb=" SG  CYS B  57 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 205 " - pdb=" SG  CYS B 231 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 207 " - pdb=" SG  CYS B 253 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.54
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2150

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      49.0% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 49
      removed outlier: 4.321A  pdb=" N   PHE A  25 " --> pdb=" O   MET A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 106
    Processing helix  chain 'A' and resid 109 through 134
    Processing helix  chain 'A' and resid 148 through 171
    Processing helix  chain 'A' and resid 173 through 179
      removed outlier: 3.537A  pdb=" N   LEU A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 188
    Processing helix  chain 'A' and resid 189 through 200
      removed outlier: 3.755A  pdb=" N   VAL A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 215
      removed outlier: 4.427A  pdb=" N   PHE A 208 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 224
    Processing helix  chain 'A' and resid 229 through 259
    Processing helix  chain 'A' and resid 261 through 265
    Processing helix  chain 'A' and resid 273 through 286
    Processing helix  chain 'A' and resid 297 through 327
      removed outlier: 4.071A  pdb=" N   LEU A 309 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLY A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ALA A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   MET A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'A' and resid 352 through 364
    Processing helix  chain 'A' and resid 384 through 394
    Processing helix  chain 'A' and resid 407 through 414
    Processing helix  chain 'A' and resid 432 through 451
    Processing helix  chain 'A' and resid 462 through 471
      removed outlier: 3.763A  pdb=" N   LYS A 466 " --> pdb=" O   GLN A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 500
    Processing helix  chain 'A' and resid 502 through 510
      removed outlier: 3.537A  pdb=" N   MET A 506 " --> pdb=" O   GLY A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 533
      removed outlier: 3.771A  pdb=" N   TYR A 527 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU A 530 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLY A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 555
      removed outlier: 3.802A  pdb=" N   VAL A 553 " --> pdb=" O   SER A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 562
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 740 through 743
      removed outlier: 4.096A  pdb=" N   ALA A 743 " --> pdb=" O   PRO A 740 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 740 through 743'
    Processing helix  chain 'A' and resid 759 through 766
      removed outlier: 3.707A  pdb=" N   LEU A 763 " --> pdb=" O   SER A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 792
      removed outlier: 3.519A  pdb=" N   VAL A 792 " --> pdb=" O   ASP A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 797
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 817 through 830
    Processing helix  chain 'A' and resid 872 through 876
      removed outlier: 4.005A  pdb=" N   ASN A 875 " --> pdb=" O   THR A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 886
      No H-bonds generated for 'chain 'A' and resid 884 through 886'
    Processing helix  chain 'A' and resid 887 through 892
      removed outlier: 3.958A  pdb=" N   LEU A 891 " --> pdb=" O   ASN A 887 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ASP A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 887 through 892'
    Processing helix  chain 'A' and resid 902 through 905
    Processing helix  chain 'A' and resid 906 through 911
    Processing helix  chain 'A' and resid 916 through 921
      removed outlier: 3.840A  pdb=" N   ASP A 921 " --> pdb=" O   SER A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 930
      removed outlier: 3.658A  pdb=" N   PHE A 929 " --> pdb=" O   SER A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 941
      removed outlier: 4.209A  pdb=" N   THR A 935 " --> pdb=" O   ASP A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 956
    Processing helix  chain 'A' and resid 965 through 971
    Processing helix  chain 'A' and resid 985 through 989
      removed outlier: 4.096A  pdb=" N   ASP A 989 " --> pdb=" O   PRO A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1008
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.882A  pdb=" N   LEU B 163 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 159 through 164'
    Processing helix  chain 'B' and resid 186 through 190
      removed outlier: 3.683A  pdb=" N   ARG B 189 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 209 through 219
      removed outlier: 3.825A  pdb=" N   TRP B 215 " --> pdb=" O   PRO B 211 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 227
    Processing helix  chain 'B' and resid 241 through 245
      removed outlier: 3.708A  pdb=" N   PHE B 245 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 251
    Processing helix  chain 'B' and resid 259 through 297
      removed outlier: 3.586A  pdb=" N   ALA B 263 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR B 266 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLY B 269 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      Proline residue:  B 270  - end of helix
      removed outlier: 3.507A  pdb=" N   LEU B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141
    Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402
      removed outlier: 3.588A  pdb=" N   HIS A 379 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   GLY A 349 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 8.800A  pdb=" N   LEU A 423 " --> pdb=" O   HIS A 344 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   VAL A 346 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   LEU A 425 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   CYS A 348 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   ILE A 484 " --> pdb=" O   ILE A 456 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   THR A 458 " --> pdb=" O   ILE A 484 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 540
    Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 779
      removed outlier: 6.282A  pdb=" N   CYS A 800 " --> pdb=" O   ILE A 879 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   GLU A 881 " --> pdb=" O   CYS A 800 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ILE A 802 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   PHE A 915 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   THR A 880 " --> pdb=" O   PHE A 915 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 976 through 980
      removed outlier: 3.978A  pdb=" N   PHE A1050 " --> pdb=" O   GLY A1013 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   GLY A1013 " --> pdb=" O   PHE A1050 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 50
      removed outlier: 3.577A  pdb=" N   LEU B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   LEU B 148 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86
      removed outlier: 3.827A  pdb=" N   LEU B  86 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    380 hydrogen bonds defined for protein.
    1062 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.15

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2449
        1.33 -     1.45: 1605
        1.45 -     1.57: 5030
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 9164
  Sorted by residual:
  bond pdb=" N   GLN A 831 "
       pdb=" CA  GLN A 831 "
    ideal  model  delta    sigma   weight residual
    1.455  1.500 -0.045 1.25e-02 6.40e+03 1.30e+01
  bond pdb=" N   GLN A  19 "
       pdb=" CA  GLN A  19 "
    ideal  model  delta    sigma   weight residual
    1.456  1.500 -0.043 1.21e-02 6.83e+03 1.28e+01
  bond pdb=" N   ARG A  20 "
       pdb=" CA  ARG A  20 "
    ideal  model  delta    sigma   weight residual
    1.454  1.498 -0.043 1.31e-02 5.83e+03 1.10e+01
  bond pdb=" CA  SER A 744 "
       pdb=" CB  SER A 744 "
    ideal  model  delta    sigma   weight residual
    1.530  1.477  0.053 1.68e-02 3.54e+03 9.97e+00
  bond pdb=" N   VAL B 229 "
       pdb=" CA  VAL B 229 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.038 1.24e-02 6.50e+03 9.20e+00
  ... (remaining 9159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 11954
        1.51 -     3.03: 397
        3.03 -     4.54: 79
        4.54 -     6.06: 17
        6.06 -     7.57: 8
  Bond angle restraints: 12455
  Sorted by residual:
  angle pdb=" N   ILE A 416 "
        pdb=" CA  ILE A 416 "
        pdb=" C   ILE A 416 "
      ideal   model   delta    sigma   weight residual
     113.07  105.99    7.08 1.36e+00 5.41e-01 2.71e+01
  angle pdb=" C   THR B 228 "
        pdb=" N   VAL B 229 "
        pdb=" CA  VAL B 229 "
      ideal   model   delta    sigma   weight residual
     122.90  116.70    6.20 1.28e+00 6.10e-01 2.34e+01
  angle pdb=" N   ASN A 745 "
        pdb=" CA  ASN A 745 "
        pdb=" C   ASN A 745 "
      ideal   model   delta    sigma   weight residual
     113.01  107.37    5.64 1.20e+00 6.94e-01 2.21e+01
  angle pdb=" N   THR A1006 "
        pdb=" CA  THR A1006 "
        pdb=" C   THR A1006 "
      ideal   model   delta    sigma   weight residual
     111.36  116.18   -4.82 1.09e+00 8.42e-01 1.96e+01
  angle pdb=" N   CYS A1001 "
        pdb=" CA  CYS A1001 "
        pdb=" C   CYS A1001 "
      ideal   model   delta    sigma   weight residual
     111.28  106.53    4.75 1.09e+00 8.42e-01 1.90e+01
  ... (remaining 12450 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4878
       18.00 -    36.01: 484
       36.01 -    54.01: 64
       54.01 -    72.01: 9
       72.01 -    90.01: 6
  Dihedral angle restraints: 5441
    sinusoidal: 2121
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" CA  TYR A1015 "
           pdb=" C   TYR A1015 "
           pdb=" N   ARG A1016 "
           pdb=" CA  ARG A1016 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.78  -18.22     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CB  GLU A 819 "
           pdb=" CG  GLU A 819 "
           pdb=" CD  GLU A 819 "
           pdb=" OE1 GLU A 819 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   90.01  -90.01     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  GLU A 699 "
           pdb=" CG  GLU A 699 "
           pdb=" CD  GLU A 699 "
           pdb=" OE1 GLU A 699 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.70  -89.70     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5438 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1196
       0.057 -    0.114: 204
       0.114 -    0.171: 27
       0.171 -    0.228: 4
       0.228 -    0.284: 5
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" CA  ARG A 972 "
            pdb=" N   ARG A 972 "
            pdb=" C   ARG A 972 "
            pdb=" CB  ARG A 972 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  CYS B 231 "
            pdb=" N   CYS B 231 "
            pdb=" C   CYS B 231 "
            pdb=" CB  CYS B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  THR A1006 "
            pdb=" N   THR A1006 "
            pdb=" C   THR A1006 "
            pdb=" CB  THR A1006 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.27    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 1433 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 159 "    0.060 5.00e-02 4.00e+02   9.13e-02 1.33e+01
        pdb=" N   PRO B 160 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO B 160 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 160 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 830 "   -0.019 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" C   MET A 830 "    0.063 2.00e-02 2.50e+03
        pdb=" O   MET A 830 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   GLN A 831 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  17 "   -0.016 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   ARG A  17 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ARG A  17 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLY A  18 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 849
        2.75 -     3.28: 9038
        3.28 -     3.82: 14619
        3.82 -     4.36: 17431
        4.36 -     4.90: 29446
  Nonbonded interactions: 71383
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 708 "
            pdb=" OE1 GLU A 709 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OD1 ASN B 147 "
            pdb=" OG  SER B 171 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   VAL A 727 "
            pdb=" NH2 ARG A 765 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" NH2 ARG B 210 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   GLN A 402 "
            pdb=" NH2 ARG A 413 "
     model   vdw
     2.287 3.120
  ... (remaining 71378 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.660
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5971
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      :  0.004   0.055   9164  Z= 0.284
  Angle     :  0.672   7.570  12455  Z= 0.400
  Chirality :  0.047   0.284   1436
  Planarity :  0.005   0.091   1574
  Dihedral  : 13.947  90.012   3279
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.82 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1130
  helix:  0.82 (0.24), residues: 468
  sheet: -0.33 (0.58), residues: 97
  loop : -0.26 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 116 
 HIS   0.004   0.001   HIS A 771 
 PHE   0.025   0.001   PHE A 511 
 TYR   0.023   0.002   TYR B 266 
 ARG   0.004   0.000   ARG A  20 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 199
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   94 MET cc_start: 0.6175 (mmm) cc_final: 0.5832 (mmm)
REVERT: A  264 GLU cc_start: 0.6344 (mm-30) cc_final: 0.6057 (mm-30)
REVERT: A  265 ASN cc_start: 0.6268 (m-40) cc_final: 0.5410 (t0)
REVERT: A  453 LYS cc_start: 0.6595 (mppt) cc_final: 0.5992 (ttmt)
REVERT: A  884 ASN cc_start: 0.7807 (t0) cc_final: 0.7408 (m-40)
REVERT: A  886 THR cc_start: 0.7231 (m) cc_final: 0.7019 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2652
  time to fit residues: 70.0780
Evaluate side-chains
  115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0470
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    6.9990
   overall best weight:    1.9884

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

Flipped N/Q/H residues before XYZ refinement:
A 772 ASN
A 831 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.214419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.178905 restraints weight = 10756.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 1.73
r_work: 0.3629 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9164  Z= 0.275
  Angle     :  0.641   7.326  12455  Z= 0.329
  Chirality :  0.044   0.151   1436
  Planarity :  0.005   0.066   1574
  Dihedral  :  4.196  16.954   1229
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.47 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1130
  helix:  0.93 (0.24), residues: 479
  sheet: -0.34 (0.55), residues: 105
  loop : -0.29 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 215 
 HIS   0.009   0.002   HIS A 771 
 PHE   0.028   0.002   PHE A1000 
 TYR   0.023   0.003   TYR A1032 
 ARG   0.004   0.001   ARG B 217 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.7120 (mmm) cc_final: 0.6849 (mmm)
REVERT: A  201 ARG cc_start: 0.6776 (ttm-80) cc_final: 0.6169 (ttm170)
REVERT: A  453 LYS cc_start: 0.6656 (mppt) cc_final: 0.6014 (ttmt)
REVERT: A  477 TRP cc_start: 0.6134 (t60) cc_final: 0.5762 (t60)
REVERT: A  886 THR cc_start: 0.8105 (m) cc_final: 0.7848 (m)
REVERT: A  930 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7183 (p0)
REVERT: A  933 ILE cc_start: 0.7870 (mm) cc_final: 0.7515 (tt)
REVERT: A  949 LEU cc_start: 0.8124 (tp) cc_final: 0.7872 (mt)
REVERT: A  955 GLU cc_start: 0.5588 (mp0) cc_final: 0.5115 (mp0)
REVERT: A 1007 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4480 (m-80)
REVERT: B  124 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5562 (tp)
  outliers start: 20
  outliers final: 10
  residues processed: 139
  average time/residue: 0.2441
  time to fit residues: 45.9346
Evaluate side-chains
  114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  901 THR
Chi-restraints excluded: chain A residue  930 ASN
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  131 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0170
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 102 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 87 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.5822

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 772 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.215721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.179309 restraints weight = 10972.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.71
r_work: 0.3630 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9164  Z= 0.139
  Angle     :  0.487   6.286  12455  Z= 0.252
  Chirality :  0.039   0.140   1436
  Planarity :  0.004   0.058   1574
  Dihedral  :  3.743  15.234   1229
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.24 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1130
  helix:  1.28 (0.24), residues: 481
  sheet: -0.25 (0.55), residues: 105
  loop : -0.13 (0.29), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 215 
 HIS   0.003   0.001   HIS A 771 
 PHE   0.017   0.001   PHE A1000 
 TYR   0.011   0.001   TYR A1032 
 ARG   0.007   0.000   ARG B  99 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A   94 MET cc_start: 0.7149 (mmm) cc_final: 0.6937 (mmm)
REVERT: A  453 LYS cc_start: 0.6487 (mppt) cc_final: 0.5970 (ttmt)
REVERT: A  477 TRP cc_start: 0.6135 (t60) cc_final: 0.5764 (t60)
REVERT: A  505 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8283 (t)
REVERT: A  739 MET cc_start: 0.6971 (ttt) cc_final: 0.6593 (ttm)
REVERT: A  886 THR cc_start: 0.8144 (m) cc_final: 0.7890 (m)
REVERT: A  930 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6928 (p0)
REVERT: A  933 ILE cc_start: 0.7826 (mm) cc_final: 0.7479 (tt)
REVERT: A  955 GLU cc_start: 0.5578 (mp0) cc_final: 0.5169 (mp0)
REVERT: A 1007 TYR cc_start: 0.5223 (OUTLIER) cc_final: 0.4695 (m-80)
  outliers start: 20
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2139
  time to fit residues: 36.9952
Evaluate side-chains
  109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  930 ASN
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 98 optimal weight:    8.9990
   chunk 97 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 907 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.209330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.172533 restraints weight = 10704.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.69
r_work: 0.3558 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9164  Z= 0.272
  Angle     :  0.587   7.362  12455  Z= 0.303
  Chirality :  0.042   0.150   1436
  Planarity :  0.005   0.057   1574
  Dihedral  :  4.102  18.322   1229
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.92 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1130
  helix:  1.07 (0.24), residues: 481
  sheet: -0.40 (0.54), residues: 105
  loop : -0.37 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 767 
 HIS   0.005   0.001   HIS A 254 
 PHE   0.021   0.002   PHE A1000 
 TYR   0.017   0.002   TYR A 928 
 ARG   0.003   0.001   ARG A 790 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7024 (ttm-80) cc_final: 0.6524 (ttm170)
REVERT: A  453 LYS cc_start: 0.6771 (mppt) cc_final: 0.6117 (ttmt)
REVERT: A  505 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8501 (t)
REVERT: A  565 MET cc_start: 0.6915 (ttm) cc_final: 0.6621 (tpp)
REVERT: A  739 MET cc_start: 0.7158 (ttt) cc_final: 0.6781 (ttm)
REVERT: A  778 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7443 (mt)
REVERT: A  930 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7045 (p0)
REVERT: A  933 ILE cc_start: 0.7870 (mm) cc_final: 0.7666 (tt)
REVERT: A  955 GLU cc_start: 0.5780 (mp0) cc_final: 0.5576 (mp0)
REVERT: A 1000 PHE cc_start: 0.4133 (OUTLIER) cc_final: 0.1971 (p90)
REVERT: A 1002 LYS cc_start: 0.6934 (tppt) cc_final: 0.6311 (tttm)
REVERT: A 1007 TYR cc_start: 0.5104 (OUTLIER) cc_final: 0.4607 (m-80)
REVERT: A 1031 ARG cc_start: 0.6976 (mtt-85) cc_final: 0.6754 (mtt-85)
REVERT: B  126 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5656 (tt)
REVERT: B  230 LEU cc_start: 0.5983 (pp) cc_final: 0.5768 (pp)
  outliers start: 24
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2491
  time to fit residues: 42.9783
Evaluate side-chains
  121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  782 THR
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  901 THR
Chi-restraints excluded: chain A residue  930 ASN
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  126 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0770
   chunk 92 optimal weight:    0.0980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.212186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.175472 restraints weight = 10795.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 1.70
r_work: 0.3574 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9164  Z= 0.129
  Angle     :  0.482   7.106  12455  Z= 0.248
  Chirality :  0.039   0.147   1436
  Planarity :  0.004   0.051   1574
  Dihedral  :  3.702  14.676   1229
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.87 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1130
  helix:  1.28 (0.25), residues: 488
  sheet: -0.31 (0.54), residues: 105
  loop : -0.28 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 215 
 HIS   0.005   0.001   HIS A 771 
 PHE   0.015   0.001   PHE A 120 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B  99 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.6887 (ttm-80) cc_final: 0.6341 (ttm170)
REVERT: A  453 LYS cc_start: 0.6638 (mppt) cc_final: 0.6046 (ttmt)
REVERT: A  477 TRP cc_start: 0.6207 (t60) cc_final: 0.6002 (t60)
REVERT: A  481 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7028 (t0)
REVERT: A  505 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8279 (t)
REVERT: A  886 THR cc_start: 0.8549 (m) cc_final: 0.8290 (m)
REVERT: A  930 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7049 (p0)
REVERT: A 1000 PHE cc_start: 0.4225 (OUTLIER) cc_final: 0.2006 (p90)
REVERT: A 1007 TYR cc_start: 0.5138 (OUTLIER) cc_final: 0.4748 (m-80)
REVERT: B  230 LEU cc_start: 0.5971 (pp) cc_final: 0.5714 (pp)
  outliers start: 20
  outliers final: 11
  residues processed: 118
  average time/residue: 0.2176
  time to fit residues: 36.1316
Evaluate side-chains
  111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  782 THR
Chi-restraints excluded: chain A residue  930 ASN
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain B residue  126 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 92 optimal weight:    0.2980
   chunk 52 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    2.0588

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.207587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.172294 restraints weight = 10720.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.57
r_work: 0.3553 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9164  Z= 0.249
  Angle     :  0.576   6.700  12455  Z= 0.296
  Chirality :  0.043   0.163   1436
  Planarity :  0.005   0.056   1574
  Dihedral  :  4.156  19.265   1229
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.59 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1130
  helix:  0.99 (0.24), residues: 487
  sheet: -0.45 (0.53), residues: 103
  loop : -0.35 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 767 
 HIS   0.007   0.001   HIS A 254 
 PHE   0.017   0.002   PHE A 120 
 TYR   0.017   0.002   TYR A 928 
 ARG   0.006   0.001   ARG B 113 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6688 (ttm170)
REVERT: A  453 LYS cc_start: 0.6773 (mppt) cc_final: 0.6175 (ttmm)
REVERT: A  481 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7210 (t0)
REVERT: A  565 MET cc_start: 0.7121 (tpp) cc_final: 0.6627 (tpp)
REVERT: A  778 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7537 (mt)
REVERT: A  886 THR cc_start: 0.8665 (m) cc_final: 0.8456 (m)
REVERT: A  955 GLU cc_start: 0.5301 (mp0) cc_final: 0.4999 (mp0)
REVERT: A 1000 PHE cc_start: 0.4442 (OUTLIER) cc_final: 0.2595 (p90)
REVERT: A 1002 LYS cc_start: 0.6394 (mttp) cc_final: 0.6187 (tptt)
REVERT: A 1007 TYR cc_start: 0.5148 (OUTLIER) cc_final: 0.4682 (m-80)
REVERT: B   62 LEU cc_start: 0.5946 (mt) cc_final: 0.5618 (mt)
REVERT: B  126 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6253 (tt)
REVERT: B  230 LEU cc_start: 0.6041 (pp) cc_final: 0.5746 (pp)
  outliers start: 24
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2222
  time to fit residues: 40.4490
Evaluate side-chains
  124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  216 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 95 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 111 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0370
   chunk 61 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7262

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.210445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.174100 restraints weight = 10772.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.72
r_work: 0.3547 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9164  Z= 0.141
  Angle     :  0.482   6.862  12455  Z= 0.248
  Chirality :  0.039   0.150   1436
  Planarity :  0.004   0.055   1574
  Dihedral  :  3.746  15.678   1229
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.70 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.26), residues: 1130
  helix:  1.27 (0.25), residues: 490
  sheet: -0.62 (0.51), residues: 113
  loop : -0.17 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  93 
 HIS   0.004   0.001   HIS A 771 
 PHE   0.019   0.001   PHE A 511 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.006   0.000   ARG B 113 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6645 (ttm170)
REVERT: A  265 ASN cc_start: 0.7256 (m-40) cc_final: 0.6460 (t0)
REVERT: A  388 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7710 (mt-10)
REVERT: A  477 TRP cc_start: 0.6078 (t60) cc_final: 0.5852 (t60)
REVERT: A  481 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7028 (t70)
REVERT: A  565 MET cc_start: 0.7255 (tpp) cc_final: 0.6819 (tpp)
REVERT: A  778 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7468 (mt)
REVERT: A  886 THR cc_start: 0.8694 (m) cc_final: 0.8456 (m)
REVERT: A  955 GLU cc_start: 0.5379 (mp0) cc_final: 0.5055 (mp0)
REVERT: A 1000 PHE cc_start: 0.4350 (OUTLIER) cc_final: 0.2205 (p90)
REVERT: A 1002 LYS cc_start: 0.6503 (mttp) cc_final: 0.6217 (tptt)
REVERT: A 1007 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4760 (m-80)
REVERT: B  113 ARG cc_start: 0.5588 (ttt90) cc_final: 0.5382 (mtm180)
  outliers start: 24
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2007
  time to fit residues: 36.6620
Evaluate side-chains
  120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 12 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 86 optimal weight:    8.9990
   chunk 93 optimal weight:   20.0000
   chunk 25 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 451 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.209227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.174189 restraints weight = 10982.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 1.63
r_work: 0.3566 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9164  Z= 0.176
  Angle     :  0.509   6.807  12455  Z= 0.260
  Chirality :  0.040   0.149   1436
  Planarity :  0.004   0.056   1574
  Dihedral  :  3.839  16.485   1229
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.42 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1130
  helix:  1.25 (0.25), residues: 491
  sheet: -0.61 (0.50), residues: 113
  loop : -0.22 (0.29), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  93 
 HIS   0.005   0.001   HIS A 771 
 PHE   0.015   0.001   PHE A 511 
 TYR   0.012   0.002   TYR A 928 
 ARG   0.007   0.000   ARG A1031 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6514 (ttm170)
REVERT: A  265 ASN cc_start: 0.7249 (m-40) cc_final: 0.6462 (t0)
REVERT: A  477 TRP cc_start: 0.6009 (t60) cc_final: 0.5761 (t60)
REVERT: A  481 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7144 (t0)
REVERT: A  565 MET cc_start: 0.7146 (tpp) cc_final: 0.6740 (tpp)
REVERT: A  778 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7494 (mt)
REVERT: A  886 THR cc_start: 0.8739 (m) cc_final: 0.8485 (m)
REVERT: A  955 GLU cc_start: 0.5499 (mp0) cc_final: 0.5151 (mp0)
REVERT: A 1000 PHE cc_start: 0.4573 (OUTLIER) cc_final: 0.2398 (p90)
REVERT: A 1002 LYS cc_start: 0.6478 (mttp) cc_final: 0.6214 (tptt)
REVERT: A 1007 TYR cc_start: 0.5210 (OUTLIER) cc_final: 0.4763 (m-80)
REVERT: B  126 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6548 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2007
  time to fit residues: 33.7436
Evaluate side-chains
  119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 94 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 771 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.209668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.174204 restraints weight = 10751.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 1.60
r_work: 0.3575 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9164  Z= 0.164
  Angle     :  0.496   6.755  12455  Z= 0.253
  Chirality :  0.040   0.159   1436
  Planarity :  0.004   0.055   1574
  Dihedral  :  3.788  15.252   1229
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.52 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1130
  helix:  1.35 (0.25), residues: 484
  sheet: -0.56 (0.51), residues: 113
  loop : -0.15 (0.28), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A  93 
 HIS   0.008   0.001   HIS A 771 
 PHE   0.015   0.001   PHE A 120 
 TYR   0.010   0.001   TYR A 928 
 ARG   0.007   0.000   ARG A1031 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7106 (ttm-80) cc_final: 0.6495 (ttm170)
REVERT: A  339 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8148 (t)
REVERT: A  481 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7131 (t0)
REVERT: A  565 MET cc_start: 0.7134 (tpp) cc_final: 0.6746 (tpp)
REVERT: A  778 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7654 (mt)
REVERT: A  886 THR cc_start: 0.8712 (m) cc_final: 0.8444 (m)
REVERT: A  955 GLU cc_start: 0.5388 (mp0) cc_final: 0.4984 (mp0)
REVERT: A 1000 PHE cc_start: 0.4593 (OUTLIER) cc_final: 0.2403 (p90)
REVERT: A 1002 LYS cc_start: 0.6465 (mttp) cc_final: 0.6123 (tppt)
REVERT: A 1007 TYR cc_start: 0.5134 (OUTLIER) cc_final: 0.4736 (m-80)
REVERT: B  126 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6554 (tt)
REVERT: B  295 ARG cc_start: 0.6095 (ttp80) cc_final: 0.5706 (ttp-110)
  outliers start: 22
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1990
  time to fit residues: 33.6257
Evaluate side-chains
  119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1049 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0050
   chunk 102 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    0.2980
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 = 0.4279 r_free = 0.4279 target = 0.211573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.177031 restraints weight = 10889.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.58
r_work: 0.3632 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9164  Z= 0.125
  Angle     :  0.487   8.682  12455  Z= 0.247
  Chirality :  0.039   0.153   1436
  Planarity :  0.004   0.054   1574
  Dihedral  :  3.618  14.790   1229
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.03 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1130
  helix:  1.45 (0.25), residues: 486
  sheet: -0.45 (0.50), residues: 113
  loop : -0.06 (0.29), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A  93 
 HIS   0.002   0.001   HIS A 451 
 PHE   0.015   0.001   PHE A 511 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.005   0.000   ARG A1031 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.049 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.7045 (ttm-80) cc_final: 0.6451 (ttm170)
REVERT: A  453 LYS cc_start: 0.6705 (mtmm) cc_final: 0.6355 (pttm)
REVERT: A  481 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.6967 (t0)
REVERT: A  505 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8289 (t)
REVERT: A  565 MET cc_start: 0.7127 (tpp) cc_final: 0.6750 (tpp)
REVERT: A  778 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7652 (mt)
REVERT: A  886 THR cc_start: 0.8656 (m) cc_final: 0.8399 (m)
REVERT: A  955 GLU cc_start: 0.5456 (mp0) cc_final: 0.4990 (mp0)
REVERT: A 1000 PHE cc_start: 0.4509 (OUTLIER) cc_final: 0.2353 (p90)
REVERT: A 1007 TYR cc_start: 0.5389 (OUTLIER) cc_final: 0.4865 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 120
  average time/residue: 0.2002
  time to fit residues: 34.2458
Evaluate side-chains
  116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue 1000 PHE
Chi-restraints excluded: chain A residue 1007 TYR
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1049 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 111 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 95 optimal weight:   10.0000
   chunk 64 optimal weight:    0.0070
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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 = 0.4275 r_free = 0.4275 target = 0.210991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.181441 restraints weight = 10853.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 1.45
r_work: 0.3697 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9164  Z= 0.136
  Angle     :  0.492   6.970  12455  Z= 0.249
  Chirality :  0.040   0.156   1436
  Planarity :  0.004   0.053   1574
  Dihedral  :  3.636  15.477   1229
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.14 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1130
  helix:  1.41 (0.25), residues: 488
  sheet: -0.42 (0.50), residues: 113
  loop : -0.05 (0.29), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP A  93 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.016   0.001   PHE A 120 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.006   0.000   ARG A1031 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4847.03 seconds
wall clock time: 86 minutes 33.33 seconds (5193.33 seconds total)